Nevertheless, Bodie & Doyle 'coming out' or being 'outed' is either implied or overtly stated in a lot of stories. The ways and means are many...
In Wish I wasn't here by M Fae Glasgow, the reader has to follow Bodie in reading the signs (no quote here - the story is available in .pdf file format only - also it's worth reading from the beginning).
In Wonderful Tonight by Sebastian, Doyle tells Kate Ross during a psychological evaluation...
She was looking back through her file, leafing through several pages. “Let’s recap, 4.5. The last time—no, the time before, I think—that you underwent this psychological profile, in the course of your ‘Partner—Relationship’ evaluation, you told me that you and 3.7 were regularly involved sexually with each other.”
His heart began to pound. Hadn’t seen that one coming. He leaned back in his chair, flipping a pen in his fingers. “Yeah,” he drawled. “So I did.”
She looked cool, unconcerned. In her job, she’d heard it all before, and many times worse. “Is that still the case?”
She was making quick checks on a chart. Her well-cut dark hair swung around the pale curve of her cheek; impatiently she brushed it back. “But, presumably, this sexual involvement drops off whenever either of you has a relationship going with a girl.”
“Not really, no,” he said, thinking that if that were the case he and Bodie would never get it together at all, since one or other or both of them was always involved with a girl. Usually several.
Dr Ross’ head came up, with that slow intent stare which meant that something he had said had engaged her attention. “So, are you saying, that this sexual contact with your partner isn’t just a substitute—a stopgap, shall we say—between heterosexual relationships?”
“No.” Was that wrong? She was writing at speed now, pen flying across the paper, dark strands of hair flicking as she wrote. He tried to read it upside down, but as usual could not.
“But, for example, when you were on your holiday with the two girls last week, presumably your sexual relationship with your partner receded into the background—”
He hesitated. “Couldn’t say that exactly.”
“Elaborate for me,” she said, dark eyes intently dwelling on him, and he took a deep breath, opened his mouth, and told her.
Half way through his account—truthful, but edited—she laid down her pen very carefully and sat quite still. And when he had finished her gaze remained fixed on him, as blank and unreadable as a camera lens scanning and scanning for information.
The silence began to make him uneasy. He didn’t think he’d told her anything all that shocking, no details: just times, places, frequency. None of the emotive words of sex and passion there, no mention of lust, desire, fellatio, nothing about the way he had whispered Bodie’s name as their bodies touched in the night, the way Bodie’s kiss had lingered, with love, on his lips—
“Let me get this quite clear,” she said at last, quiet and uninflected, “You and 3.7 take two girls away for, what, four days. In that time you have sexual contact with your girlfriend, twice, and with Bodie, six times.”
Put like that—
He shifted uncomfortably. “Yes, but it wasn’t—” It was all far too complex to explain. ‘Bodie took me by surprise.’ ‘The girls were out.’ ‘Susanna wasn’t in the mood.’ all sounded in the analytical light of day like poor excuses indeed.
“Anything wrong with that?” he asked aggressively, going all out for attack.
She shook her head briskly. “How you manage your personal affairs isn’t a matter for me to make moral judgements on, Doyle.”
He picked on the word instantly. “So you are sitting there thinking I’m immoral?”
“Morality is of no concern to me,” she said coldly, “except as to how it affects you. And more specifically, how it affects your performance in the job you’re paid to do, ergo how it affects your relationship with your partner. Just one more question, 4.5—”
He grinned at her, mocking. “Got it in one. You want me an’ Bodie to take you away for a weekend in Scotland.”
“—which of you usually takes the dominant role? I mean here,” she added, pen poised, “in a purely sexual situation.”
“Neither of us. Either.” She was always hinting at some sexual ambiguity in him: fortunately it didn’t bother him one bit. If you played both sides of the line you had twice the fun, that was how he saw it. But he was damned if he was going to give her what she was angling for and confess that he played the girl in bed to Bodie’s he-man, because it didn’t happen to be true.
He left the session feeling, as always, vaguely moody.
In Heat Trace by Helen Raven they are exposed suddenly and very publically.
Bodie was already on his feet. As the crowd of young men parted to let Doyle through, Bodie took one look at his expression, and stepped forward, arms open. Doyle’s helmet fell off as he pressed his face against Bodie’s neck.
“Shhh, Ray. It’s alright. I’ve got you. Shhh. It’s alright now, love.”
After some seconds of disbelief, the CI5 men moved to close the gap, screening the pair from the rest of the pub. Bodie was facing the room, his eyes nearly closed at first as he concentrated on Doyle, murmuring reassurances and endearments, stroking the curly hair with unmistakable tenderness. Doyle’s face was hidden from sight.
Bodie raised his head in time to see Lucas heading away from the group into the body of the pub. Towards the ‘phones, probably. He was quite calm as he glanced around the circle, meeting any eyes that cared to meet his, indifferent to any expression of contempt or triumph or narrow-eyed speculation, or simple surprise. Ray was all that mattered. He lowered his head again, waiting patiently for Doyle’s grip to ease, for some sign that he would soon be ready to move.
“What’s this about, man?” Cowley had arrived in the pub. Bodie heard no reply to the question, but the group shifted once again.
Bodie had not often seen the Scotsman at a loss for words. They stared at one another for several seconds, though Cowley’s eyes kept flicking to Doyle. He probably didn’t recognise him, or not directly, but there was enough information for him to make a reasonable guess. In the end he returned his gaze to Bodie, and after a frowning examination, opened his mouth.
“Yes, sir. It’s exactly what you think it is.” He felt Doyle become tense in his arms. Ray probably wasn’t fully aware of what was happening, but he would know that Bodie’s attention had shifted, and that would disturb him. Bodie continued the gentle movement of his hands, and drew Ray closer. It seemed to help.
“Why like this, 3.7? Are you trying to ruin the department?”
“This was an accident. And it’s got nothing to do with the department. You were never supposed to know.”
“That does not make this any better.”
“No, sir, I know. Look, I’ll tell you everything, sir, but, please, not here. Not now. I have to take care of Ray. Tomorrow. Please.”
“You won’t be in the country tomorrow. I know the contacts you have.”
“No. I won’t run away. Because I’m not frightened. I know what I am, what it means. Put a tail on me. You’ll see.”
After a long pause: “My office. Eight in the morning.”
“Thank you, sir.” But Cowley had already turned away, and was making his way out of the pub. Bodie turned his full attention to Doyle again.
In Benevolence by Brenda K, they out themselves - by accident!
(no quote, because that would be way too spoilery *g*)
In Undercover Activities by O Yardley they decide to tell Cowley together (this is the last story in the Party Spirit series - worth reading from the beginning).
"In view of this last job, sir," I said, pricking this bubble of preoccupation with deliberate pleasure, "we thought we ought to have a talk with you concerning a possible security risk."
That brought his head up as I'd meant it to. He barked, "Well?" pulled off his glasses and waited. I'd no intention of being hurried, nor of standing in front of his desk with Doyle like two fourth formers carpeted in the head's study. This promised to be a long and stormy interview so I grabbed one chair and waited until Ray was settled in another before turning to face the Old Man eyeball to eyeball.
"It's a personal matter," I expanded. "Ray and I would rather you heard it from us ... not from anyone else ... not that anyone else is aware of it but ... the fact is we have .... that is, er, we ..."
"What Bodie's trying to say is that he and I are lovers," Ray interrupted, offering me a blinding smile when I looked his way, surprised at the easy way he came out with it. It was a nice line though, and it disconcerted Cowley considerably. Very satisfying. I've been trying do it for years but never with such outstanding success.
"You and Bodie are ..." He broke off, stared from Ray to me and back and then said disgustedly, " Och! if this is your idea of some sick joke ... "
"No joke, sir," I assured him." We're perfectly serious."
The look of disgust deepened. "Then I hope you have both come to your senses by now. I presume this happened some night when the pair of you were drunk ..."
I shook my head. "Actually, it began several years ago -- but it's only recently become serious and exclusive."
"Several years?" Cowley sounded incredulous. He glared at both of us impartially. "Are you telling me the pair of you have been involved in a homosexual relationship for that length of time and have only just seen fit to inform me of the fact?"
"Wasn't anything to tell you about before," I protested.
"Nothing to tell me...."
I was starting to get annoyed. "No, sir, nothing. What we do in our spare time's not your affair...and before you say it, just tell me where it says in the small print that I have to come bleating to you every time I get me end away."
Personally, I have difficulty with the idea that Cowley would smile benevolently, offer his best wishes (and a bottle of pure malt), and give a speech at the wedding. I'm not saying he would react badly because of prejudice, but he would be concerned to protect CI5 at all costs, a priority that would be well ahead of the well-being of his agents. That said, anything's possible in fan fiction!
Also, harking back to some previous discussions about gay politics in the 70's and 80's, today I stumbled across an interesting paper about James Anderton's Manchester (connections to the episode "In the Public Interest):