I don't think the vibration will be that much of a problem. A drive shaft application is not like stirring a beaker, where the stirring rod can also act like a free-swinging pendulum.
In this case, if you have bearings on the drive shafts by the magnets, and another bearing on the prop shaft by the prop (in addition to a strong motor mount), the vibration should be kept to a minimum because the prop shaft can't move (except for rotation).
I agree, though, that once you lose sync you have to stop the shafts and start slowly from zero. And if your sub is negatively buoyant, you might just sink your sub before you can get the prop(s) restarted...