Damage to crew is moddled by damage to barge from rifle and light MG bullets that hit the "top", in reality these could not even damage the steel hull but they do in the game signifying damage to troops from bullets that come in from a higher elevation, we are not talking about swift boats here which are made from tinfoil.
fig. 1 (imagine a much smaller scale version but with steel hull, this is the barge that lifts your AFVs)
To sink barge with rifle and MG simply have a squad or MG at a higher elevation then the barge, higher the better.
fig. 2 (I've actually been on one, maybe about a half inch of steel)
You could be right about them taking too many large caliber rounds to die, one hit below the water line from 90mm should over come the bilge pumps and destroy it over the course of some turns.
There is no way to model below water line hits, As Don or Andy will tell you this is not a turn-based naval strategy game.