Their main problem, in my opinion, from what I've read recently in my research for helping keltos01 out with the Climb Mount Niitaka mod, is that their "management" were stuck in a 1905 "Kantai Kessen" mind-set ("Naval Fleet Decisive Battle"). The submarine was a scout and a warrior. It was not to be used to sink lowly merchant vessels. Not only that, but since they were such good scouts, they would make great troop and supply transports, especially in shallow waters with a plethora of US DD vessels to shoot at on the way out...
- No! Wait! We change our minds! Instead of Guadalcanal, let's send you to Kiska!... Yeah, that's the ticket, Kiska... ahh yes, I remember her well... Kiska, such a good kisser... sigh...