It has nothing to do with "shipping". That's a separate thing fans do. There are a few analyses written on Tumblr, one in particular, is a 2 part "meta" or analysis written by "Cassbel5" and there is also the interview Louise Brealey did with Masterpiece that basically point to things happening off screen. These things are only hinted at. We aren't shown them. And in many instances they are things that aren't witnessed by John or any of the characters that are part of Sherlock's inner circle. Every time these 2 characters appear together or are spoken about in the same breath, their relationship is somehow different, but we're not shown how. An example of this is Molly's flat, specifically her bedroom being used as a bolthole by Sherlock; there isn't much said about it, just that it is the case. But that is a red flag that should have gone up. You have to ask yourself, at what point is it reasonable to allow a man to take over your bedroom if you aren't in some kind of relationship that's more than a simple platonic friendship? This isn't a reasonable expectation that any man would ever have even by modern standards if he wasn't involved in significant way. Again, it's an "arrangement" arrived at without John's knowledge. This is important because John, as Sherlock's blogger/chronicler he doesn't know everything there is to know about his friend. And we're shown that. How is it that the only one who doesn't know Sherlock's birthday is John? Regarding the Canon, there has been some discussion about John as the "unreliable narrator". I think in some ways, this series took that idea and ran with it. How well does John really know his friend? For that matter how well do any of us know our friends, our significant others, our siblings or our parents? Go find that meta and read it. Its very interesting.