Is the HI cost that significant? I would be concerned about the extra supply to replace the aircraft and the loss of a few more of your best pilots. The only advantage of the 1E night fighters I can see (apart from the option to resize air groups) is they use up less space at smaller bases.Given the number of losses in airframes that the 4Es cause, I'd rather use and lose 2* the number in Zeroes/Judys than in Irvings. Unfortunately, the IJAAF only has 2-engine versions.
Looking at my Tracker, there are actually 2 groups other than the Endo Detachment (321 Ku S-1 and 321 Ku S-2) that can only use the J1N1-S version and no others. The rest can all choose from any of the other IJNAF 2Es or the C6N, and only 4 groups are allowed to use the A6M or D4Y frames (3 each). It's worth noting that you can probably resize those 3 units...
PDU On, I think all the groups can use any model once they have changed to a night fighter model. However, there are some groups that need specific models in order to change to using night fighters.
I haven't yet had to counter the B-29 but against the B-24 the only night fighter that seems to pull its weight has been the J1N1-S. Not sure why the Ki-46-III isn't performing well.