Hm. So, well, I usually try to avoid the Hiatus as a plot thing, but it might be for the best here.
I’m thinking John isn’t married. This was an indiscretion, and he and the mother are like, “Haha, marriage is NOT a good idea.” But you know, he’s not the kind of guy who’s going to bail out on his kid, so he and the mother are trying to hash out a workable system.
And then Sherlock comes back. And it’s just—BAM. All the feelings they’ve been sitting on for the past *mumble* years. John doesn’t really mean not to tell him; it’s just that things are nuts. Sherlock’s return has turned John’s life upside down, they’re in a relationship where the emotions are all over the place…it’s a mess.
So he’s still in that “Uhm…when and where is a good time to bring this up?” stage when Sherlock does his Sherlock thing and is like, “Were you planning to tell me about this at any point?” And then there’s another morass of emotions, because John loves the goob but he’s going to need time to get over the whole Hiatus thing, and now here’s Sherlock getting huffy that, y’know, Life Happened to John in the meantime. And Sherlock’s ticked because he’s feeling aggrieved about John still being mad, and also kind of insecure because, well, where does he fit into John’s life now?
So there’s a bit of a clusterfuck and Sherlock not really getting parenthood and maybe being a touch jealous that he has to share the spotlight in John’s brand of devotion. And oh yeah, the mother probably gets to meet Sherlock at some point and there’s some mutual, “I have to deal with this person in my life?” dubiousness.
But it all works out in the end, and there’s some surprisingly cosy non-romantic domesticity and everybody works out their own corners to live in.