The Japs had some creepy plans for the Aircraft carrying i-400, here's their original intention:-

For their first mission Vice Admiral Jisaburo Ozawa, Vice Chief of the Navy General Staff, selected Operation PX, a top secret plan to use SubRon One's ten aircraft to unleash bacteriological warfare on populous areas of the American west coast and Pacific Islands. Infected rats and insects would be dispersed to spread bubonic plague, cholera, dengue fever, typhus and other plagues. General Ishii's infamous medical laboratory at Harbin, Manchuria, had developed the virulent germ warfare agents and confirmed their lethality by infecting helpless Chinese and Caucasian prisoners

Perhaps they had a rat breeding colony on board the sub?

That's an amazing piece of information/speculation.

Even if the infected animals had failed to spread plague, just publicising their release would have had way more effect on the minds of the American public than simply dropping the half-dozen bombs that those planes could carry.

They were never used on submarines, but to control the problem Battleships and other surface ships frequently had a cat on board that became a member of the crew. Besides being friendly with the sailors they did a supberb job of keeping the rat population on the ships down to a minimum.