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Later ones got under wing bombs.
Perhaps the Japanese didn't want to take the performance hit of a pair of Ho 103s in the wing. A pair of guns with just 200rpg goes about 79kg without links, ammo boxes/chutes, mounts, local reinforcement, charging systems, etc. Not a lot of weight but then the Ki-43 didn't have a lot of power.
I see the logic in your statement but I have to point out that the Ki-43 used the same engine (Nakajima Ha-25) that the Zero did and the Zero had 20 mm cannons in the wings which did not hamper it's performance in any way. That is why I think it has something to do with the actual structure of the wings internally (if you look at any drawings of the wings of the Ki-43 they don't look any less thick than other contemporary fighters of the day).