My Sims are pausing every once in a while and all NPCs seem to have been stuck somewhere?

The Sims 3 is notorious for high CPU and resource usage, especially when you get multiple households and things going. Try opening up the task manage (ctrl+shift+esc) while playing and take a look at the CPU and Memory percentages. If they are pegged at 100% or close to it, that may be the problem.

The game does try to "optimize" by instead of the entire game chugging, only certain processes of it do, like sim behavior and the background world simulation (which is why everyone is tired). Something to try is lower the various settings, or removing households you don't really care about so the background simulation doesn't have to work as hard(backup your save in case this doesn't work!).