I found and sunk one a couple weeks ago, just outside of Balikpapan in February, 1942. One torpedo sent it to the bottom. My crew called out "She's going down, sir!" and I watched it disappear. A red "sunken ship" label showed up on the map, but when I exited the game it only gave me credit for the tonnage, but not a warship kill.
I still added a Rising Sun flag to my sail, though!
Sometimes you don't get credit for sinking in-port ships because they hit bottom without going completely under.