This currently is set-up to emulate that confusion... The player will generally be 'penalized' for all sorts of stuff. I wouldn't insinuate the submariners were disorganized, but the upper ranks most certainly were, and incompetent in their use of the force - thankfully. If you take those few weeks of success they had around Guadalcanal, or in the Indian Ocean, and have a procedural limit on shooting range for the torpedoes, and they could have created havoc on the Seas. But they were not allowed to fight, and when they were, they were sent against warships in congested areas with heavy ASW (not too dis-similarly from the US effort at the beginning of the war). Add to that the fact that the US had cracked the comm codes, and knew almost to the yard where each of the IJN subs were from basically 1943 onwards, and you can see why the IJN sub picket lines were "rolled-up" almost every time. When they weren't, the US went around them... Throw in some Mk27 mines, the IJN late war tactics, and it was a recipe for disaster. The links below are not meant as "shopping" links, but only as examples:
The Japanese Submarine Force and World War II
I have that one (link is now throwing an error... ??) and when the Japanese surrendered, their submarines were in deplorable condition, lacking even rudimentary necessities, such as functioning toilets. The machines stunk to high-heaven. Lack of material and maintenance... "Here fellows, here's the latest technology of the Empire. Now go an do your duty for the Emperor"...
Another of interest to me, and on my "Christmas Wish List" is
Sunk: The Story of the Japanese Submarine Fleet, 1941-1945
War is always a waste of humanity, but the Japanese submarine force losses were staggering.