The air pump in a bubbler is meant to run 24/7. The plants will become overwatered if you turn off the pump, as the roots cannot get enough oxygen and your babies can get root-rot. As for the rockwool being constantly in contact with the nutrient solution; you want to lower the nutrient level so that the roots have about an inch or two of air space between the net-cup and the nutrient solution as soon as your roots are long enough. Hope this helps.

L0rdsOth