That's exactly why I developed the mod, to get rid of that whining sound which seems to be an indication that the ship is slowly sinking!
Indeed, I used the mission editor to test "convoys" of different ship-types, looking for those ships that emitted that whining sound. Almost inevitably, any ship making that noise will eventually sink. So, I started tweaking and ended up with my sinking ship fix. So far, I have only tested merchants and one or two military types like the LST.
Thanks for reminding me that some ships sink without player intervention even at stock settings. Although I made my changes so the ships would not sink even with the wave-heights set to 2X via SH3 Commander, the ships seem to work just as well at stock settings. So, I think you can use the mod with either stock or altered settings via SH3 Commander.
If using the mod at stock settings, one possible problem
might be ships that seem harder than normal to sink. I, however, have not personally observed this potential problem.