The 'scare' shortage is caused by two main elements; a lack of skilled Scarers (note also that most of the monsters going through Monsters University with Mike and Sully aren't particularly scary) and a door shortage caused by an increasingly large number of unscareable children.
Waternoose looked around the room in frustration. Human children were getting harder and harder to scare. Monstropolis was in the middle of an energy crisis. Right now, Monsters, Inc. supplied most of the scream energy for the city. But if he didn’t get some good Scarers soon, his company might go out of business!
Monsters, Inc. - Official Novelisation
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.
Note also that there are multiple scare floors set on a variety of levels of the building...
image courtesy of Monsters Inc. Essential Guide
...so it's entirely possible that scaring is happening elsewhere in the building (complete with its own infrastructure) while Mike and Sully's floor is shut down for the night.