Especially after your population contracts European diseases against which they had no immunity. Early Spanish records say they passed endless villages and cites along their journey up the Amazon. Two decades later, no villages or cities or people were seen on the same river route.
Yes they were all occupied some point. Else why would any one build?
Large populations require storage, markets, etc. How many buildings are actually occupied outside of work hours today?
Why would extensive civilizations be any different?
Places of worship--not habitation.
Markets--not habitation.
Warehouses--not habitation.
Government buildings--not habitation.
Libraries and centers of learning--again, not habitation.
So some percentage of the structures involved will not be habitation space.