In this 2010 trial from Australia, they compared a variety of types of veggies grown in three systems, identical except for the method of supplying water:
Timed Flood and Drain (15/45 min)
The result from this small 18 month trial is that timed flood-drain wins, hands down, across most plant types with faster plant growth, more worms, and larger fish. It also used less energy since the pump switched on and off.
The constant-flood and bell siphon systems traded back and forth for 2nd place. In the end, certain kinds of plants did better in constant flood and others with the siphon.
They provided no explanations for why they thought the results were what they were, though others made a lot of speculations across the 40-page thread. They were trying to be un-biased, so avoided making judgments.
I have a constant flow flood/drain system that usually cycles every 10 to 15min or so. My fish and plants seem like they are in heaven!
The fish have been spawning over and over in there.
I have an extremely low fish stocking density though. I make up for it by feeding the fish on auto-feeders 4 times a day. That way they are able to consume the required amount of food to feed the plants.