The scare shortage is caused by two main elements; a lack of skilled scarers (note that most of the monsters going through university with Mike and Sully aren't particularly scary) and a door shortage (with children who aren't able to be scared any more).
Just fifteen years earlier, Monsters, Inc were able to run scare floors night and day, as evidenced by the full car park during this night-time break in.
As to why they don't run floors with semi-skilled scarers, that should be fairly obvious when you see what can happen to even an experienced scarer who's a bit lax.