actually the Germans tended to send their subs round with stuff on board for the Japanese. They did send a full Me163 rocket fighter, but that sub was sunk. The Japanese did indeed make a 'copy' of the Me163 from some drawings that did get through.
You've got to feel that a well used submarine fleet could have been a war winner for Japan. America isn't vunerable to the same kind of commerical warfare as Britain but every thing it needs to wage war against Japan has to be shipped a very long way to reach it's fleet in the Pacific. If the Japanese make support ships the main target its going to force the Americans to to divert more resources to protect their support ships. This might not necessarily change the course of the war but it probably would have been more productive.
One reason the US Navy was able to provide so many escorting destroyers to the carrier task groups was the lack of a viable Japanese submarine threat. More and more as the war went on Japanese subs were sent on supply missions to cut off Japanese garrisons on bypassed islands all over the Pacific. Many were lost on these missions.