I believe it was upgraded from none to little
13mm head/back armour, 65mm armoured glass canopy, and a self-sealing fuel tank. It was as well protected as any common fighter aircraft of the era.
...
From an empirical point of view, the pilot wound in the Ki-84 is indeed far more frequent than any other plane I've flown - frequent enough to warrant a complaint.
However, there could be fairly simple explanations as to what is causing such frequent PWs. One such explanation being;
...at least in my case, about 99% of the PWs I've experienced while flying the Ki-84, was during a sharp breaking turn to evade enemy fire. Since such a turn typically exposes the top portion of the cockpit which is unprotected by metal armour plates, the frequency of PWs under such conditions are entirely understandable.
Especially, since many pilots take note of the superior low-speed turning characteristics of the Ki-84, there is a high existing tendency of pilots who know how to fly the Ki-84 well enough, to use aggressive turn-and-bait tactics to lure the attacker behind him into a stall fight - and quite often, these pilots will attempt to draw in the enemy until dangerously close distances. If the tactic fails, and if somehow the enemy behind (at least momentarily) gains an angle sharp enough to make out a firing solution despite the superior turn of the Ki-84, then the Ki-84 exposes the top of the canopy at a very slow speed - which makes it a sitting duck.
Consider this:
If it was any other plane - perhaps a Zero, or a Hurricane, or even a Spitfire, you'd just be dead, and that would be the end of it. However, because the Ki-84 is a well protected plane, one might survive such an attack and take notice of the occuring pilot wound - and might think that PW occurs to often in the Ki-84, despite the fact that in any other plane, one might simply be pilot-dead, and instantly return to the tower.
If it was any other plane that didn't turn so well as a Ki-84, one would also simply be dead, since the enemy plane behind you would gain enough time for a steadier gun solution that would rip the plane to shreds. However, because it was a Ki-84, the enemy had only a brief moment to try to land a shot on you - and since the Ki-84 did turn well enough to evade most shots and get hit by only a few (albeit critical) shots near the canopy, you might survive it, and then notice a PW... and naturally be misled to think that the Ki-84 shows more PW than other planes.
...
Therefore, unless there is a definite, controlled test done concerning how often the Ki-84 falls to PW under which circumstances, I cannot really say there is a PW problem with the Ki-84. It might be nothing but a simple distortion of perception as to what happens with the Ki-84s.