Just an fyi, autotracking works with torpedos which was a very pleasant and unexpected surprise. I'll be upgrading my maxed out Demon with it's 10 torps to the Centurian with it's 40 torps shortly Talk about firepower...
Internally proton torpedos are treated as a gun with limited ammo, with all that it implies (autotracking works, can't shoot them down, won't show up on radar...)