Your leak is likely between the skimmer and the pump (suction side not pressure side).
Have you checked for a vortex in your skimmer, sometimes all it is is slightly lower water levels allowing some air in.
You may also have a leak in your pipes anywhere before the pump or even the pump lid gasket could require some lube.
Outside of those areas, it's highly unlikely you'd suck air anywhere post pump, instead you'd be squirting water.
I doubt you're damaging anything with some air going through the system.