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The Japanese giant submarine could carry one more bomber than could any of ours at the time. Obviously not much, but enough.

Now for the atom bomb design the Japanese were using, it was very likely a two stage device similar to one we now have under development.

Although it looked to be quite feasible back in the early 1940s it proved to be a "dud" ~ rather like the device the North Koreans recently tried to get to work. In fact, it's dollars to doughnuts that the NK device IS a refurbished Japanese WWII device, or a device based on their design.

Our plutonium and uranium bombs were very heavy and difficult to build. Big difference between our bombs and the Japanese bombs was that ours worked.

BTW, with the Japanese bomber launched from just offshore from one of their giant submarines, they probably could have dropped half a dozen atom bombs (of their, not our design) and really upset us.