I did some personal testing and tweaking on the ship damage model before deciding to switch to 4.11.1m version (I'm anxiously awaiting 4.12m and plan to switch to that once SAS gets an activator out for it... multi-turret functionality for tanks is something I've been hoping to see for a long time, and with it I'm sure we'll see the modders here go to town with adding bow MG to tanks and so forth). Anyway...
I experimented with tweaking the entire system for ship damage. In short, I wasn't really happy with most of the mods around... I felt that to be realistic, the ship's damage should be modeled so that MG fire would be effective against the unarmored superstructure of ships, and unarmored guns, but not the hull.
I remembered what one veteran said in an interview... "If you want to put a hole in a ship, use a bomb. If you want to sink it, use a torpedo."
So I went in and tweaked the strengths of the ships overall so that only the largest of bombs could sink a ship, but machine gun fire and small bombs could do lots of damage to the rest of the ship. How?
To do this I created a separate class of strength types, and tweaked the stats for each of them.
Strength_Hull - For 'Vital' Parts which represent the actual ship's hull.
Strength_Structure - For structural parts like smokestacks, radars, and structural components.
Strength_Gun - For the various turrets mounted on the ships.
I'm thinking of going back and redoing this and posting the ship.ini information if you'd like. Though I often find that deciding what would be realistic for some things is something that could be up for debate... for example there are multiple accounts of machine gun fire from aircraft knocking out tanks by hitting the engine deck or even bouncing up through the floor. How do you account for pure flukes of luck when you assign penetration values? I mean, a 37mm gun might not penetrate the front of a tiger normally, but what if it goes through the driver's port?
Lots of things to consider.