The houses are built cheaply with minimal insulation and no internal air (every room is heated/cooled independently, if at all, often with gas burning heaters that emit the exhaust directly into the room). When the wind blows it blows through the building. Houses don't last more than a few decades and are torn down. Houses are depreciating assets in Japan, like cars.
Edit: Yes we need to deregulate and dezone housing laws, especially in major metropolitan areas in the US, however that's not what causes Japanese housing to be cheap. It's apples and oranges and different expectations among the populace on what a house even is.