Understand you idea but would make the pontoon floats a lot bigger I think. The thruster bottom will only be about 6" from the surface and they can be deployed out from the boat but just lowering the wings, it will only be a few pounds overall.
To have the thruster in the pontoon it would need to be drawing a lot of water itself.
With only 10-12lbs of thrust on the pontoons there wont be a lot of stress. This isn’t moving at high speed.
But this may all have to be rethought once we start testing. The thruster idea may not work at all.
Ideally the thruster will be right on the bottom of the float but I expect it may need to be lower to ensure it remains below the surface.