My opinion is that the lack of a specific 'depiction' of how things happen leads to confusion or misconception. I've been monitoring how cockpit damages happen in various occasions, and it seems how the pilot was wounded is always shrouded in certain depths of confusion in most cases.
For instance, the game currently uses only three 'damage sounds' to depict what was hit where. There's;
1) 7.7mm~.50, 'hit sound'
2) cannon 'hit sound'
3) 'damaged' sound
Now, when a certain bullet hits and drills the windshield, it uses the same 'damaged' sound as any other part - there's no way to tell if a bullet hit the windshield and that cracked it, or some other reason caused it. (nearby flak burst, collision, internal ricochet after being hit.. etc etc)
Another fact is that the damage depiction inside the cockpit is minimal. In certain cases where the pilot was wounded, it is easy to tell how the damage was inflicted, since you can at least approximately track the path the bullet entered, by looking at the bullet hole in the windshield.
However, in those other occasions such as;
* a bullet hit from underneath the plane and cleaved through the seat
* a bullet hit from sides and penetrated the side of the cockpit
* frontal attacks from HOs or GV pintle guns
etc etc.. there's not sufficient damage depiction to track just how or where the pilot was hit.
The final problem is the question; how is pilot damage dealt in the first place? I'm pretty sure HTC uses a 'pilot figure' as a damage model part, and a bullet hit to it will cause damage. But what if the bullet hits legs? arms? shoulder? head? The information on different levels of damage according to where the pilot was hit would be nifty to track out just how the bullet entered the cockpit - except we don't have this info, and however the pilot was damaged, it is always the same black outs.
What if there was internal damage depiction? For instance, if a plane without a frontal engine block such as the P-38 or a Mossie gets hit while ground attacking, if the bullet came from forward, it would have had to puncture through the dashboard to hit the pilot. There would be some instrument that was damaged - and by this, we could figure out just what caused pilot damaged.
What if there was differing levels and symptoms of pilot damage? If your control input becomes sluggish or weak while no flight surfaces are damaged(aileron, elev. etc.. ), one might guess the pilot was hit on the arm, and would only use one arm, and this would slow down input in high-G or high speed maneuvers - in this case one would also be able to figure out where the bullets hit and how.
All in all, its the lack of depiction which makes suspicious that something might be strange. If more detail and depiction was put into the game, it would turn out that nothing is really wrong with the game. At least, that's my opinion.