After the experience i just had, i woudlnt recommend upping the hitpoints. Least of all on the bulkhead.
Behold, the results of a circular running torpedo

This, is what should be left of my engine room. I should have been sunk, but wasn't.
Yup, i had alot of engine damage, but the bulkhead was unscratched, and i had no flooding. All i did, was take the bulkhead hitpoints, and change it from 100, to 400. I used 400 because it seemed logical to make the bulkhead as tough as the compartments in the zones.cfg. Said compartments i changed to 400 hps, because thats what it was in SH3.
I honestly don't think bulkhead hitpoints should be raised past 200, and i mean seriously, look at the damage thats being rendered. Nobody survives that. My boat should be at the bottom of the Java sea right now.