Was the proximity of the Ki-43's replacement, the Ki-44, in terms of delivery schedule, a component here? Ki-43s had only just entered service by the time of the Malayan Campaign and yet there was a small detachment of pre-production Ki-44s also available for that conflict. Why invest in up-arming the Ki-43 when the Ki-44 was so much more capable?
Maybe part of the problem was that production for the Ki-44 did not ramp up sufficiently quickly...or delays in retooling from the Ki-43 to the Ki-44 were too costly in terms of productivity? Certainly the Ki-43 was retained in service for far too long when more capable designs had been available for years.