At some point, waterproof shaft seals will fail. The problem is that even if a shaft seal mates well with a shaft, the rotating motion of the shaft inevitably causes momentary pathways for fluid to leak through, and with enough pressure (enough depth), water will push its way past the seal and into the motor housing.
Once solution to this issue is to avoid running a shaft through the waterproof interface altogether. The concept is called a Magnetically Coupled Drive and its most often found on large-scale, industrial ROVs that are intended for use in very deep water. Similar technologies can also be found in the food processing industry as well as in medical equipment. Here's how they work:
Instead of spinning a propeller directly through a shaft, the motor spins a set of magnets that are in a completely sealed container along with the motor. Wires needed to power the motor do not move, so they can enter the water proof housing through potting.
Side cross section, and angled diagram of magnets attached to a gear motor which is encased in a sealed cylinder.
A second set of magnets are mounted inside a ring with an inter diameter just slightly larger then the outer diameter of the cylindrical waterproof motor housing.
Front and side cross section of outer ring with magnets surrounding inner magnets attached to motor shaft. Note that magnets are configured in alternating polarity- this provides greater torque transfer both allowing opposite polarized magnets to attract each-other, but prevents skipping by repelling neighboring magnets
The outer ring can be used as a hub for propeller blades or to transfer motion to a propeller elsewhere. In the configuration shown, there is very little normal force between the two surfaces, so bearings are not needed and abrasion is minimal.
Here's what I built with actual hardware. I intend to post instructions on how people can build these soon.
600 RPM 12v DC gearmotor with inner magnet rotor attached
Right: Motor/ magnet assembly placed inside cylinder- top will soon by potted. Left: outer ring with magnets installed and propeller blades attached. Note, mineral oil was originally used to make the motor housing less compressible, but it turned out to be more of a mess then it was worth and eventually caused the motor to cease.
Here's a video of the thruster working in a bowl of water. The motor used only draws about a tenth of an amp, however the thrust level is not particularly high.
First test of Magnetically Coupled Drive in water. Propeller held in place at end of video to demonstrate that magnetic coupling also helps prevent motor burnout if debris or other problems cause stop the propeller from being able to spin.