My experience:
First patrol: photo recon of Osaka. On the way in at night a shore battery opened up and I dove to PD. A harbour escort was alerted and came to check out the fuss, but I eluded him. On the way out the sun was coming up so I was trying to stay as deep as possible and scraped the keel a bit in the shallows. No damage report or loss of speed so I thought all was well.
Inexperienced crew on SD or bug: I got jumped by Japanese aircraft without warning, and contrary to other's experience posted here, they proved to be very effective causing considerable, but not immediately catastrophic damage to my boat. The flooding is represented by "water" in the affected compartment's name box on the damage screen.
I took damage to the aft bulkead, the entire drive train save the screws and rudder, and of course the main pump

The boat went down stern first quckly so I attempted to abort the dive, and had to blow tanks to get her up. I thought I'd lost her but putting priority on the pump and bulkhead and keeping her at flank kept me afloat. I found that some items were repaired quickly (pump and bulkhead, but only to a certain degree), but others not (diesels, electrics, decoy discharger). It was taking a long time to pump the water out and the boat was down at the stern so I resigned myself to the fact that I could not take her down and would have to fight it out on the surface if anything came along.
Sure enough, more aircraft showed up. At flank I could only do 13 knots, and despite my efforts at manouvering and the AA downing one of them, I was the recipient of another bomb hit which immediately sank my boat.
I liked how it went through a series of camera views of the boat going down, but then a screen came up saying I had been court martialled and sent to the brig for sinking a friendly vessel?!
I sank 6 merchants during my mission, positively ID'd everyone one of em and they were all indicated as enemy vessels in my log. I wonder if I may have caused initial damage to the boat when I scraped bottom and then because of that got credited with my own sinking? :hmm: :rotfl: