Historically, there was some rare case of sub vs sub warfare:
I would say that in a strategical level game like A&A it is not so revelant.
That’s why I find the No subs vs subs a fine rule.
http://en.wikipedia.org/wiki/HMS_Venturer_(P68)
On completing trials and working-up, Venturer commenced operations patrolling the Norwegian coast for coastal traffic and U-boats leaving or entering base.
She was successful on several occasions, sinking three Axis vessels during 1944.
She also sank U-771 on 11 November 1944 7 nautical miles (13 km) east of Andenes, Norway, off the Lofoten Islands.
Her most famous mission, however, was her eleventh patrol out of the British submarine base at Lerwick in the Shetland Islands, under the command of 25-year-old Jimmy Launders, which included the only time in the history of naval warfare that one submarine intentionally sank another while both were submerged.
Sent to the Fedje area, Venturer was then ordered on the basis of Enigma decrypts to seek, intercept and destroy U-864 which was in the area. U-864 was carrying a cargo of 65 tonnes of mercury and Messerschmitt jet engine parts to Japan,[2][3] a mission code-named Operation Caesar.