Plain old cheap plastic storage tubs from a dollar shop do just fine. Most are transparent plastic. My transparent tanks, located under my flood trays, don't get enough light to cause any problems. If you get algae accumulating in the tanks, cover the sides with panda film to block light.
A 125L (~33 US gallon) tub will do nicely for a 3'x3' tray. No need to modify the plastic tub at all; the pump & overflow drain hoses will be fitted to the centre of the tray, just above the tub. No fittings through the tank wall means no leaks.
You'll be hard pressed to find tubs much bigger than 125L, so just use two 125L tanks for your two 3x3 trays. A 3x3 tray which floods to about 3-4" will empty about 1/2-2/3 of the volume of a 125L tank when flooding. A 3x3 tray full of mature plants will use about 1/3 of a 125L tank per week. Smaller tubs in such a system will require you pay attention to water level more than once weekly or the tank water level may become too low to fully flood the tray (pump may suck air).
