Turning the key off on your Yanmar kills power to the alternator "ignition" wire as well as engine instruments. This ignition wire turns off the Hitachi's internal regulator
and stops the alternator from producing current
This will have no affect on the engine or alternator. The engine being entirely mechanical (including the stop cable) will continue to run. Other devices- lights, sailing instruments, etc will be powered by the ship's batteries and will ultimately run down, but this is no different than while sailing.
As others have said, this is very different from disconnecting the batteries while the engine is running. If you do that the alternator which was producing charging
amps suddenly has no place to put those amps. This causes a momentary voltage spke which blows the alternator's internal diodes. A Zap-Stop device, another diode, can prevent this from happening.