Basket Depth in PVC System

[Pawnic]

Hey there you fish scented green thumbs!

I just set up a small pvc system, and I'm worried the holes for my baskets are too small. Right now the roots sit in about 1-1.5 inches of water for an hour cycled at a time. The roots are beginning to grow out of the baskets, but i'm wondering if the plants would improve greatly sitting deeper in water. Everything is healthy and seems to be growing just fine nonetheless. Just looking for improvement. 

On a second note...

Does anyone have any experience root fertilizing in this type of system? Any suggestions?

-Pawnic