Is the flat bottom wing better for water take-off/landing on sponsons? That would be a good justification for a flat wing trainer that I could upgrade to a water plane later on.
The high wing more so than the airfoil I would say. Properly attached floats give any wing the positive incedence it will need for lift. Getting the step where it ought be and keeping the wing up where a rouge wave can't tap it are more important. Trainers usually have "long legs" and a high wing that help on both snow and water.
I will say this: at our club's float fly 80% are flat bottommed wings.