Those plane carrying ones are buggy in stock I heard. I THINK ive sunk them with one or 2 torps using RFB. My memory may be bad though

You also have to look at the dark side of why the large and impressive looking Japanese submarine fleet accomplished such meager results in comparision to the Germans and Americans.

Although there is no evidence that the Japanese had any qualms about attacking merchantmen, Japanese submarine doctrine strongly emphasized attacks on warships. This was in keeping with the Japanese focus on the decisive battle that was supposed to be fought between the main Japanese and American battle lines somewhere in the Western Pacific. In order to compensate for the anticipated numerical superiority of the American fleet, the Japanese planned to wear down the Americans with attacks by submarines, light surface forces, and aircraft as the American Fleet crossed the Central Pacific. As a result, Japanese submarines did not initially concentrate against the long and vulnerable Allied supply lines.

This was unfortunate for the Japanese. Although their submarines had some notable successes during the war, particularly the sinking of the Wasp during the Guadalcanal campaign, the employment of Japanese submarine forces was characterized by inflexibility and indecisiveness. A particular weakness was the use of ever-shifting picket lines, which persisted long after these had proven vulnerable to Allied hunter-killer groups, which were often guided to their victims by Ultra intelligence. Some of the poor management of Japanese submarine forces may have arisen from the fact that the submarine staff officers, even at the highest levels, were no higher in rank than commander, and so had little clout.

Another misuse of Japanese submarines was their employment in transport operations to isolated garrisons. This became the major activity of the submarine force after 16 November 1942, when all available I-boats were placed under the command of Mito Hisao at Rabaul to carry out supply operations (mogura, "mule", operations) in the Solomons and New Guinea. A seaplane-equipped I-boat could carry more than fifty tons of cargo in place of its aircraft facilities. However, the runs were extremely unpopular with the submarine crews, whose morale plummeted. With their hangers being used as a cargo hold, Japanese submarine seaplanes saw little use after this point and were usually assigned to shore duties.

From November 1944 on, the emphasis switched again, this time to the use of Kaiten suicide torpedoes against Allied bases or (from April 1945 on) sea lines of communication. This proved costly and ineffective, with several of the mother ships sunk before they could deploy their Kaiten.

I've seen several Japanese submarines docked in port but I've never shot at one. Do you even get any tonnage for sinking one?

Yes.

I would say that the japanese knew that the allied merchant fleet passing under the range of their sub bases were not so vulnerable and accessible to their subs in many aspects. This may explain their primary target being warships.