Well, it could also have to do with the actual structural components of the aircraft. IIRC, Widewing was talking about how the Zero series didn't have a continuous spar that ran through the fuselage. It was actually 3 pieces bolted together at the wing root. This was apparently a result of the Japanese lacking the ability to cast a single piece spar.
Taking that idea forward, and I'm just guessing here, that as the shortage of raw material and decrease in manufacturing potential as the war went on, they may have had to make certain design tradeoffs that weakened the structure--not by manufacturing quality control (which as I understand it isn't modeled in AH) but rather simple constraints placed upon the design as a result of lack of either materials or facilities capable of making the parts the plane should have had, had the designers been able to create the structure they wanted.
Perhaps?
Anyone know if there was favortism shown Nakajima versus Kawasaki by the Japanese government? Perhaps Nakajima received more materials and manufacturing support than did Kawasaki? (Niki being Nakajima while Ki-84 was a Kawasaki product).