There is a way to fix that. It is relatively easy, too. I haven't explained this in a long time so bear with me.
Go Here:
http://www.subsim.com/subsim_files05/patches2005.html
Download Wolfies SH3 Tweak Pack. There will be instructions in the readme for a "cheat" of sorts, so check that out. It changes the Tweak Pack so it can edit the torpedo loadouts. Open the Tweak Sub program (I think that's the name). Choose the IXD2. Change the fore external reserves from 8 to 6. Then, to regain the 2 you got rid of, increase the fore internal reserves by 2. Be sure to save it. The changed loadouts will have no torpedoes in the loadout. You can leave it like that and change it in the game, or you can change them in the Tweak Pack. Presto! All fixed!