just a guess

No footpaths or streets were used between the dwellings, which were clustered in a honeycomb-like maze. Most were accessed by holes in the ceiling and doors on the side of the houses, with doors reached by ladders and stairs. The rooftops were effectively streets.

• this would protect houses from any animal that can't climb a ladder or the wall itself (also if they pull the ladders up, from anyone who doesn't have a portable ladder)
• if houses are constructed in clusters, that would mean one less wall to build (maybe 2)

I read that it was for cooling. Doors and windows let a lot of the cool air escape.

Defensive reasons, probably. Ladders can be pulled up and enemies frustrated in that way, leaving no way to get in short of bashing down the house's walls (a much more tedious and slower process than kicking down a door).