Summary

This is a proof of concept of the watertight magnetic coupling for two separate axis. It is done by using 12 Neodymium magnets, 6 on each side, arranged in alternating magnetic orientation. I used leftover magnets from some previous projects and they are around 20 mm, 3/4 inch diameter. You also need two standard 608 ball bearings.
There are two types of pins, ones that require hole through the membrane (pins A and B) but are self aligned and the universal pins that you glue to membrane without a hole but require manual alignment. To make it fully watertight pins that require hole should also be glued to the membrane. My advice is that you print them slightly elongated along the Z axis and then "slice" them to proper length where you feel that magnet bearing part is at just the right distance from the membrane. Here is the video of coupler in action: https://youtu.be/cVqbwt13msw
The last picture is the result of me trying to determine the strength of the coupling, it is rather strong and it was the shaft printed at 30% infill that gave up first. Membrane is also just for testing purposes, I imagine that some type of nonferrous metal, or rather nonmagnetic, would be used in practical application.
Propeller used for demonstration is customized: https://www.thingiverse.com/thing:116974/#files