Finally I had time to add few more sources and revise the text. One of the sources even mentions fuel tank extinguishers was used by some Ki-21, Ki-48 and Ki-49 bombers. All three types remained in production to 1944.
It’s possible that their line of thinking was that since fuel would be consumed from the wing tanks first (which I don’t know if its the case), by the time they engaged in combat those tanks would be empty and wouldn’t need self sealing protection.
CO2 extinguishers were there just in case you got jumped, and the fuselage tank still got you home.
That would have likely been the case on short range interception missions. J2M had most of it’s fuel in the fucelage tank after all. Some document even mention early J2Ms having removable wing tanks. Even so the decrease in fuel tank capacity is stated as the main reason. While production N1K2-J had self-sealing wing tanks, they still wrote down what the fuel capacity would be with plain unprotected metal tanks.