I have had a couple of Nippon Maru tankers sink to the point where only a small amount of the stack was above water. Waited a day, keeping the ship within about 5000 yards. Never sank until I went back and put one more fish into it. This has happened to me a couple of times.
I also had one time where the ship disappeared from the chart screen, but the sunk marker didn't show up. There were a couple of destroyers milling around. I knew where the ship should have been so crept back to the area. Raised the scope but kept it under water. The ship was playing submarine. This time only the top of the mast was exposed and its search lights were still on and searching. One more torp at close range (targeted with the scope underwater) finally sank it.
I've also had a couple of cargo ships go vertical, but not sink. They still showed up on the chart as living ships. I waited until the escorts left, surfaced and used the deck gun to sink the "buoys". One buoy fired its deck gun back at me. That crew must have tied themselves to the gun.
Tom