Its probably just going to delay it. If the grow is long enough, and the roots are not kept too wet, they WILL go to the water source eventually. Last time, when they were down low, it took maybe 6 weeks or so to start covering up the nozzles. It was so bad I was forced to move them to the top of the chamber. The roots still tried to get to the new locations, but I won the race that time.
The trick is regulating how wet the roots stay. If they stay very wet, droplets form on the tips of the shoots. The root then thinks its found the source and trys to grow further into that drop of water and will follow that drop all the way to the floor very quickly - they cab grow several inches in just a few days in some cases. On the other hand, if kept just right, they will form fuzzy hairs and can grow any direction at will - out into space for several inches with no support at all. Its pretty amazing.
I think the foam sheets would work well for the top of a flood chamber unless its too large. You could always add some plastic legs/supports near the net pots if needed.
Just be sure to get the solid/extruded foam and not the expanded foam. The polyurethane foams are more toxic if burned, and not as strong, I prefer the polystyrene types like this pink Owens Corning foam. It also comes in blue which is less dense and not quite as strong.
This foam absorbs very little water over time and should hold up well. I havent had to really clean mine yet other than a quick wipe down, and this is the third grow with this piece of foam. I see no signs of mold or nasty crap building up, so Im happy. Roots that stick to the lid while growing easily wipe off once they dry up a bit. I had a huge mass of roots grow from one wet spot on the lid where a nozzle was keeping it wet. Grew to be quite a mass before the roots fell off and then they just hung in space.
HDPE board would be an excellent choice, but its $$ and heavy and requires real tools to cut and machine. The insulation board can be cut with a utility knife.
nicely said 
