When a ship passes over you, you can only hear the propeller revolution, nothing else! Sometimes if the target is fast the submarine shakes a little bit. Not an engine sound you can forget about that!
As for the rest that you say, I think you state it correctly, but in order to catch up all these you need much imagination because there is not much experience on something like that. I can say you for example:
1.The warship's propeller beating is more sharp, and the flow noise also sharp, because the surfaces of warhip's hull are more frequently cleaned that the merchants.
2. A fishing boat usually has a two stoke engine and a very fast rotating shaft (difficult to count beats) and generally it sounds like "tttrrrrrrrrrrrr"
