I have suspected that chunks do not account for time passing when you are close enough for them to update again... but do not have enough proof of this, so maybe have experienced similar.
And indeed yes, certain monsters (I have no idea what their names are; they have spikes out of their back and shoot a long metal rod at you) appear to be unaffected by night or a storm ending. Seen this for sure. I do not have enough experience with the game to know if this is a bug, but if you are saying its not normal, and yea other types disappear, than you are probably right.