The scare shortage is caused by two main elements; a lack of skilled scarers (note that most of the monsters going through Monsters University with Mike and Sully aren't particularly scary) and a door shortage caused by a lack of scareable children.

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.

https://www.youtube.com/watch?v=NJOE3GgAH7o&t=55s

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.

https://www.youtube.com/watch?v=cUFJ1yVhJ6g