I think the theory behind gunnery % affecting score is based on a couple of things:
1. In some aircraft, it is much easier to score kills if you don't care about conserving ammunition and you 'lay on the trigger' for every low % gun solution you get.
2. It is a sign of a high degree of gunnery skill when you can fire a (short) burst of gunfire and a very high % of your fired rounds impact an aerial target that is not flying in a straight line. One of the best feelings for me in AH is when I fire on a tough snapshot, and I am actually sweating the timing, and the first rounds of the burst hit the nose of the target and the last rounds of the burst finish somewhere along the fuselage.
Having said that - what everyone else said in this thread is basically true. lazs is right - gunnery % is very easily 'manipulated'. Score categories are used by most (including me) as a way of tracking various trends in AH as performed by the tracker.
I think the reason for gunnery % affecting score a little may be an attempt at a deterrent - a way of assigning a little negative feedback for the person who would 'empty the clip' at 999 yds. in hopes of landing 1 or 2 'magic bullets'.
I don't know if it 'works' or not. The tough thing about it is that sometimes you would be flying 'smart' and/or 'realistically' to burn your ammunition on a shot at 999 yds. - 4 miles from the English channel, your buddy is in a P-51D and a Bf 109 is in gun range. You are going to blow thru and keep screaming for England. Your buddy is starting to dive for safety. I'd fire at very long range - scare off the Bf 109 or keep him distracted for the couple of seconds it takes your buddy to make his diving escape...
What I'd be interested to know is if there was fewer rounds fired per sortie in AH since they instituted the gunnery % affecting the score.
A good way to look at it is this - take a good gunner. Put him in the F4U-1D. Barring vulching, killing PT boats, all kills scored are bounces vs. unsuspecting targets, etc. - if he burned all his .50 BMG ammunition for 4 kills on sortie #1, and burned all his .50 BMG ammunition for 11 kills on sortie #2 - *theoretically* he was working harder for each kill on sortie #2. He was putting more work into setting up higher % gun solutions, he was 'sweating the timing' more on snapshots, etc.
But I agree with another post - the main use of scoring categories is for you tracking you in various different ways.
It would be damn interesting to see what happened to K/T, K/D, and K/S if all kills vs. targets spawned for less than 3 minutes or so were disallowed (with regards to stats), wouldn't it? When I first started playing AH I was surprised a few times at how someone ranked so high in the fighter category could be such a pushover in a real contest of maneuver and gunnery.
Mike/wulfie