as far as electric motors go, the less they have to turn off and on the longer the pump will live. I speak from experience. I fix larger water pumps and turbines (the ones u see pumping the water at water parks) and those are made to run continously. As for these aquarium pumps, they're built on the exact same concept, just smaller.
When a pump turns on, it requires double the amps, i.e. therefore more is required of the motor, vs. just leaving it on. Think of it like this, if you had to push a car..would u want to push it a block, stop, push another block, stop..or push it all the way with no stops? it's easier to keep something going...