I guess the other issue is that for instance the "several tanks could not be blown" issue would affect depth control - and there's nothing in SHIII other than flooding that affects it, meaning flooding is the only workaround for it. Things like 'hatch cracked' would also possibly imply some water being taken on.
Although if it bothers you, I think you know what to change
Just drop the flooding chance figure to a much higher damage requirement, and off with it.
Myself, I really never minded the flooding issue as it is in NYGM right now. I seem to be getting little flooding with the exception of direct hits (which makes me wonder if somehow I still have the pre-hollywood zones file... not sure why that would be, I did update it to the latest release version) :hmm: