In the case of the A6M5b, I believe that material considerations played a factor. There was a shortage of 13.2mm guns and/or ammo, so each aircraft was given one 13.2mm and supplemented with the 7.7 on the basis that it was better than nothing.
While I admit the Japanese planes are the ones I know the least about I have read that the 13.2 was unreliable,it wasnt really a machinegun and was called an autocannon as it fire explosive rounds.
These rounds caused problems,blast shields were installed so you wouldnt blow your own motor up and they jammed quite often so it was often only the 7.7 that you could rely on. This is one of the reasons the KI43 was most often found with 1 of each gun!
As was said some firepower was better than none!
Oh and IRL they had a great damage model.......