Season 3 poked fun at some of those headcanons with the Sherlock fan group and their theories on what had happened. A literal tumblr ham planet suggested Sherlock and Moriarty were trolling John together "and then they kissed". At least the rest of the group looked at the fujoshi like the mental case she clearly was but as you point out a lot of the problems with that show stem from how long it took to make so few episodes.