When I'm doing my daily chores, there is always one villager I can't find, sometimes even two!

I check everywhere. The museum, the shops, even villager houses. Nowhere to be seen.

Does anybody know of the pattern of villagers in terms of being in and out of their house? As far as I'm aware there isn't one. Some days I play and over half of my villagers are inside their houses, and other days only one villager is in their house. Is it just completely random?

Yes, it's completely random where your villagers can be. If you can't find a villager, save and quit multiple times until you find them.