Okay, just had a look into the coastal vessel; I can confirm that it is the boat depicted in your screenie.
Her hydrophone soundsource controllers are in order. She uses NF_boat_hyd.wav as engine sound, and Propeller_4_hyd.wav as propeller sound. Just in case, I have also checked the above wav files, and they are played correctly. So the problem must be somewhere else.
The boat has a max speed of 9 kts, max engine power of 500 bhp @ 90 rpm. Maybe they are too low, or maybe the boats had too a low speed compared to their maximum speed (the game cuts ship sounds when they are sailing at too a low aengine ratio), for them being audible on hydrophone. You can try setting a custom mission with the boats sailing at their maximum speed.
PS: wish Macardigan was around
