To expand on the previous answers, this happens during the day as well. You just don't realize it because you're paying attention to other things.
Typically, creaking noises in the house are due to the contracting and expanding of the various materials inside your house (Glass, wood, concrete, etc). They expand/contract at different rates throughout the day with changes in temperature and such, so that's what causes the creaking, popping, etc.
Your house is expanding and contracting due to the change in temperature.
The interior of your house might be maintained at a constant temperature, but the exterior isn't.
Different materials expand and contract at different rates which causes the floor planks, glass, heating ducts, etc to crack and pop.