Usually all ships during wartime operate with 'closed watertight' doors, so hitting it in the hold areas, when the hold is already full with cargo, doesn't make that much difference.
Hitting the boiler room and rudder areas does make a difference..
Having said that, I haven't read of that many ships surviving more than 2 torps, whereever they're hit, unless it's obviously way off.
The only resulting effect that NSM and RFB mechanics have introduced is the time the ship takes to sink. Now I'm not sure of the records, but most tough ships have been known to sink within 30 minutes, if not, it's not likely to sink. This from reading some records.
This is where both mods tend to stretch the imagination somewhat.
