I allow my pumps to run constantly, turning it off only if there is a clog in the pump. I feel the constant running helps maintain the humidity, and I have a false bottom setup/waterfall so the waterfall and bog at the bottom of the waterfall filter act as a biological filter (an awful lot like a powerhead filter on an aquarium).
So far, my pumps (I use Little Giant fountain pumps and ViaAqua "submersible water pumps) have been running for about 3 years without any trouble.
As Bryan indicated above, most clogs can be cleared by backwashing the system (pouring some water down the outflow tube while the water is turned off).
-----
Purveyor of Trivialities and Fine Nonsense