While I wouldn't be in the habit of telling someone the best way of doing things, especially not if you have good results, I would say that excluding the .303s from a burst on the enemy will mean a decrease in critical damage, especially on snapshots.
Ditto....many times all I get is one chance and generally it is a very short burst. I want that to be as effective as possible, so much so that it negates the any advantage I get from knowing with certainty which rounds are the tracers I'm seeing by only firing cannons. I do normally keep my shots in the D200 range or just as it flips to D400 (300 yds) so varying ballistics aren't that big a deal.
Just a couple mgs alone are more than capable of damaging the engine, taking control surfaces or wounding/killing the pilot (or just shaking them up a little), even on planes like the K4 or Ki-84. So I shoot em all, even though I have primary and secondary mapped independantly. The exception is the longer shots at 600-800 to try to get a plane to turn.
As a side note I remember seeing a film of Leviathn just busting enemies in a D3a with one short burst by shooting wings off at close range. While that is more the exception than the rule gunnery effectiveness is more about accuracy, range, convergence and shot placement than big guns alone. It is possible to be effective with lightly armed planes.