I've seen a lot of good reasons and idea. I think this one was missed:
the room is empty, because nobody's in it right now.
Consider your house as a dungeon. Is there somebody in EVERY room all the time? Not in my house. I don't even have enough occupants to fill all the rooms (though I do have enough stuff).
people and crittters who consider the area "theirs" move around through-out the day.
It is therefore concievable, that the distribution of monsters is really saying "this is where they are, at the time the PCs encounter them", rather than drawing up a complex documentation explaining their movements and patterns.
I would assume that if you had 6 orcs and a dungeon floor with 6 rooms, each orc would claim a room as their own if they could (assuming they felt safe that this floor was 'theirs'). A PC party infiltrating a dungeon, and needing to stop for the night, would probably instead hole up in 1 room, to maximize their safety.