So, I ship a lot of things, but I'm also always telling people to make sure to keep what is fanon separate from what is canon, because people who ONLY talk about their OTPs and how magical and so-close-to-being-canon they are actually bother me.
Their are so many hints that are legitimately written into the ship, including all of the other characters seeming to make countless gay innuendos that Sherlock either ignores or just doesn't care about, and John frantically denying any sort of relationship with Sherlock.
Two: The writers have planned this, introducing John and Sherlock as normal characters. (Okay, Sher isn't normal, but just go with it) who have lives outside of their sexuality. Just because a character is gay, doesn't mean that character's life is centered around a sexuality. They are normalizing the characters so that when it is more socially acceptable to be homosexual/bisexual/pansexual/straight but with an exception, they can introduce the relationship without it even being a shock to anyone. They won't lose viewers that way, and it would go along with the show's whole 'Haha-bet-you-didn't-see-that-coming-because-good-luck-trying-to-follow-anything-in-this-show' thing that they always seem to have going on. The 'subtle hints' that fans find would suddenly all come together, but it wouldn't be more exciting to the average viewer as a mystery being solved. (Note: A fangirl isn't an average viewer) Think about the hiatus. The Reichenbach Fall premiered on January 15th, 2012. The Empty Hearse was first shown on January 1st, 2014. Sherlockians all know this, but unless you live in England, or are part of the LGBT community(Me!), you may not know that there had been a battle to allow same-sex marriage in England for awhile, and in July of 2013, Parliament finally gave the a-okay for gays to marry, thus making homosexuality more of a norm. (*Note: The legislation was passed in July 2013, but didn't come into effect until March 13, 2014.) Remember when the big hype started when Sherlock was filming? The dates are all pretty close, so yes, I do believe that eventually, the writers plan to listen to the fangirls and have our favorite homos kiss.