Hi UberDemon and thank you sincerely for your kind interest trying to find a solution.
I do not have JapanCat's Ki-43, I just installed your Ki-43 right on top of a clean 4.09+UP2.01 install, without any further mod, and got the problem. Currently, I removed your Ki-43's and checked with stock ones (I think UP2.01 does have stock Ki-43) and can't replicate the glitch.
Honestly, with all respect for members who state they have no problems with your Ki-43, I get what looks to me a logical evidence of a wrong damaged mesh on your Ki-43-I. Must be said that the glitch is not so easy to get and happens only when fuselage is hit.
Sorry. I hope that soon or later you or some other talented guy will fix and possibly assemble in a sole pack a "true" Ki-43 series, one of the most ill-treated ones of Il-2, virtually from ALL points of view (flight model, performance, variants, loadouts).