Frederf, I don't know about SH4 but in RL I think you're on the right track. Not sure about the S-boats, but AFAIK all the fleet subs had the diesels driving the electric motors, i.e. the diesels never drove the propeller shafts directly. Any difference in efficiency must lie in charging efficiency versus motor efficiency, and I don't know which was the bigger loss-- as you said, if they were different the diesel rpm could be optimized in either direction.
But, the US WWII sub hull and propellers were optimized for surface running, not submerged running. IMHO if you're not losing efficiency in the drive train, you're losing it in hull drag underwater, and you still won't get the same mpg as on the surface.
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