The idea is not flawed! And believing in it is not intrinsically irrational. You’re absolutely right; the show gives plenty of evidence. God knows, there’s a lot going on in Sherlock, and also around Sherlock, to support the theory. And given how Moffat has demonstrated and outright admitted that he sometimes lies in order to preserve surprises in the show, the fact that he has claimed no such thing will ever happen fails to serve as solid evidence to the contrary.
So don’t feel ashamed or apologetic for believing in it! You don’t need to try to soften your opinion. You’re making sense.
The only beef I’ve ever had is with going overboard and claiming that not believing in the johnlock conspiracy is equivalent to supporting heteronormative structures. Which, obviously, the vast majority of tjlc believers aren’t doing at all. Most of you guys are just hanging out and having a grand time right along with the rest of us. So keep doing that! I love you, and I feel like you’re carrying a torch of hope. ^_^