I just descovered this tread and I'm a bit late...
The best way to waterproof an electic motor is to house the motor tight in a torpedo type metal enclosure with fins mounted around it, to cool the motor. The rear needs a flat plastic closure, install powerfull magnets on the drive side of the motor as close as possible to the interior of rear plate. On the other side mount your propeller system with same type magnets towards the interior magnets, so the interior magnets drive the propulsion unit.
The outside propulsion unit would need some kind of trust bearing, maybe even a water type bearing system, also the motor would have to be able to handle the magnetic pull towards the outside unit.
This system can be made to handle some large depths.
Roy