Sorry for the double post but I've recently come to the realisation that it might have to do with culling!
I sort of found myself reading about some "no culling mod" and the description mentioned how annoying it was to have blanks in your family tree because of ghosts being culled! And I just thought, wait... It's about culling?
So I'm not sure how EA's culling actually work, it's very abstract to me, but basically if the amount of townies reaches a certain number, sims just get culled (NPCs and ghosts, I don't actually think alive sims in the world get culled). I think the culling completely deletes the sim, has if he never existed. So if the sim culled was a ghost for instance, he'll become blank on the family tree because it's like he was never there in the first place.
SO, I decided to deactivate culling (I have MCC) and wait a while to see what happens to my family tree. Since I recently started a fresh save, might take a little while to have a big enough tree. It should show if the cousin branches get lost after a while because someone got culled, or if it's related to something else.
Since my game will no longer regulate my population, I'll have to do it manually and go to manage households to deleted NPCs here and there when it gets to crowded.
Anyway, just thought people with the same issue might want to give it a try as well. I know that Neia's "no culling" mod is no longer updated, so i'd say don't use that and go to MCC...