I was kinda worried about that too so what I did is after week 4 I switch the pump from one outlet side to the other every week and so far I've never had a roots clogging the water flow or any water leveling issues with the other bins. Plus I have a mesh screen covering my pump just in case.
Bushbaby11
This is my set up I strongly suggest going rdwc since you're familiar with dwc. It will save you a ton of time feeding at the reservoir instead of each bin (been there done that). I usually keep the cuttings in the clone box for about 2 weeks until roots are long enough around 4-6...
Get yourself 17 gal storage bins cut the top for 15 slots with 3in net pots. Do the nutrient math with 15 gals of water and you'll have 60 plants in a 4x4 without any issues.