Sinking 2 - 3 Ships in a convoy attack is realistic enough. Historically, the lower tonnages were not so much due to misses or pumping large loads of torpedoes out, but lack of contacts. IN SH3 finding targets is easier than in RL. Usually we return to base with empty tubes and plenty of fuel left. Historically U-boats returned short of fuel and torpedoes left in the tubes.
So this is a question of playability vs historical accuracy.
Now do what Onkel Neal says to do on this thread:
http://www.subsim.com/radioroom/showthread.php?t=129239