John’s stopped correcting people about their assumption that he and Sherlock are a couple. Why? Well, it doesn’t really matter what people think, particularly not in this case. They’re nowhere near home, these are people John will never see again, it doesn’t matter if they think Sherlock and John sleeping together. So why bother correcting this fellow? It’s pointless.
This is the first time we see John decide to stop correcting people on this point. And given that he starts to, as if by habit, and then changes his mind, this might be the first time he has ever made that decision.
This scene, obviously, comes after his frustrated “we’re not a couple!” to Irene Adler. He is exasperated that time around, exhausted and annoyed by the (likely constant) assumption. And Irene corrects him. Given the look on his face then, I think he took that correction to heart on some level. Because she was right: they are a couple, even if they aren’t a traditional one.
You can read this scene as an echo of that conversation, as an acknowledgement of Irene’s assessment of them. The truth of their relationship is too complicated to explain to a man who runs an Inn in Dartmoor and just handed over a room key. It’s not the kind of thing there’s any simple language for. John’s not about to sit down with a perfect stranger and explain the whole thing. So there’s really only one option: just smile and nod. Close enough.
But it’s slightly more complicated than that. As we know, John appears to have given up on dating at this point. He had a string of girlfriends Sherlock rhymes off in Scandal, but no more after that. It was too obvious that he couldn’t keep track of them, and that Sherlock was always his top priority anyway. The women weren’t so into that arrangement, as it turns out.
So he’s stopped. What made him do that? Was it his girlfriend dumping him for being such a good boyfriend to Sherlock? Or was it Irene’s honest and truthful assessment of them? He acknowledges that his life isn’t compatible with long-term relationships (except for one). He has, in effect, chosen Sherlock. So is it wrong that someone thinks they’re a couple? Not really. They are, exactly in the way Irene suggested they were. And John’s hesitation can be read as his acknowledgement of that.
The owner of the Inn is apologizing to John over the lack of a double bed in their room. What does this suggest? John tried to book a room. Not two rooms, one room. If he had led with, “I’d like to book two rooms,” and the owner said, “Sorry, I only have one available, but it’s got two beds in it,” he wouldn’t have assumed John and Sherlock were a couple in the first place, and he wouldn’t need to apologize for the twin beds. So John must have asked for one room, assuming a double bed. So John intended to share a double bed with Sherlock.
In sum: John has stopped dating, has stopped correcting the assumption that he and Sherlock are a couple, has arguably accepted that he is in fact in a long-term relationship with Sherlock, and books a room anticipating sharing a bed with him.
This, my friends, is canon.