Yes the IID is a great little boat, its agile submerged and surfaced, it crash dives faster than anything else in the game. Also, speaking from some small experience with them, you try and get an ASDIC fix on a Type II to drop depthcharges on it... its flipping hard!
Though, I have to speak up here, currently you are using just the base game patched to 1.4b which is what we all use, though some use supermods on top, or just the base game and some additional extras so to say. I'm not trying to belittle your playing here or anything, because I started out on Stock game to 1.4b too. But air craft cover in base game is, a joke, it really is laughable. As I say I don't mean to sound arrogant or conceited or anything or belittle your playing but most of us here have been used to various supermods GWX, WAC, NYGM or something of the like... so its made us quite battle hardened. I doubt any of the supermod players could ever return to base game, but anyway thats enough supermod plugging out of me.
The main danger that aircraft pose to you is they will kill your men, the uboats in stock are actually bullet proof they don't take hull damage from bullets. Of course if they drop a bomb and hit you, expect muchos damage then.
Though coming back to the type II again. In actuality, they DID carry 3 reloads more often than not. They were designed for two, but they would cram an extra torpedo somewhere into the torpedo room to bring the load out up to 6. This I do believe is modeled in the aforementioned supermods, I know for facts its in GWX. The official supermod thread is here
http://www.subsim.com/radioroom/showthread.php?t=115089
it has links to NYGM, WAC, and my personal faves... GWX and Uberboot. Check em out, and see which could be the mod for you.