I think it had very much to do with the fact that Hiashi and Hizashi were twins. That causes a lot of issues, and that's probably why they had to separate the two into different houses. Hinata and Hanabi have a 5 year difference between them, and this probably is the reason that they're both included in the main house. Or it could just be that every so often, every few generations or so, the houses are split. So it doesn't occur with every generation. Hiashi and Hizashi just happened to be born in one of those unlucky generations.