The AI makes this thing difficult. If one watches gun camera footage of attacks against shipping, you do notice a couple of things:
1. the AA is usually accurate, you see tracers very close to the attacking plane
2. the aircraft don't make themselves easy targets - they turn into attack, fly straight only when they aim and then shoot very quickly, then turn away
The Flak guns should probably be more accurate in SH3, but the airplanes behaviour should also be more complicated.
(Not that I'm an expert on SH3 airplanes. I've faced two airplane attacks without crash diving immediately. At both times the airplanes dived pretty much straight at me making themselves very easy targets - not that they weren't dangerous.)
I've solved this problem by just diving everytime I see an airplane. There is a time in 1943 when BDU gives an order to shoot it out with the planes, though