Check this out:
The warhead power in torpedoes hasn't changed much since WWII, something like 600lbs vs 650lbs, in case of MK14 and MK48 torpedo. Also, from most all information I've read, including from first hand accounts like Capt. Edward L. Beach, USN, one (detonating!) torpedo was usually enough to blow the target to hell. Neither Small Freighters, other Merchentman nor Destroyers were BB's like the Yamato. The Torpedo is a tool made specifically to destroy ships in a war. Freighters were not designed for war, and Destroyers were just tin cans. I don't know where the notion of "about 2 torpedoes seems right" comes from.
Oh and bigboywooly, the effect you describe is real. However, for numerous reasons including the ones given above by Woof1701, this is just a "fact of life" and true for all simulations. If we were to try and "nerf" simulated "careers" as per your approach, we could as well go ahead and shoot with rubber bullets in flightsims. Do we want to simulate an authentic "kill board" or a weapon system in a simulation? Anyone answering "both", is free to go and kill himself after being sunk in the sim.

Will make for more authentic tonnage counts, no doubt.