Oh, they added armor and self sealing tanks once it was pounded into them that it was a good idea after all.
The A6M2, B5N2 and D3A1 (and I am not 100% positive about the bombers) are the only Japanese fighters in AH to lack any protection at all. The A6M5b has a little pilot armor. The Ki-61, Ki-67, Ki-84 and N1K2-J all have pilot armor and self sealing tanks.
By the time the Japanese did add armor though they had lost the core of their excelent pre-war pilots and they never recovered.
One of the things the Ki-61 was built and accepted into service for was to deal with the American tactic of diving away from the Ki-43s, which like the A6M could not follow a P-40 or F4F in a dive.