Yep, a 'double crew' is a special case of course. There were several examples of this when a boat ran aground. Darter, Sail-36 and a few others I believe.
Those water cases were believed by some to be the result of chlorine accumulation. When depth charged the tanks would be shaken up and the water would make the crew sick, though evidently that was specualtion and no official cause was determined.
In the general sense I do not think food should play a part in SH4, unless we can have victory cakes made for each sinking
Maybe on S boats, but running out of food was simply not an issue on US fleet boats in my opinion (with a normal compliment that is) except perhaps in a few isolated cases.
In my opinion morale should be a function mostly of how successful the boat is (a combat insignia pin is a big morale booster) modified by how often or intensely the boat comes under counterattack. Mechanical breakdowns could play a part. A smooth running ship is better than a bucket of bolts for morale. Another morale factor is the base chosen for refit. Submariners were much more happy to go to Pearl or Brisbane than Midway, Saipan or Guam for example.