Hm, i think the problem might be related to how the game works regarding direct targetting and vicinity targetting.
If you direct target a ship and try to use the flak, it wouldn't work because it tries to apply it on the target you are directly targetting.
If you used vicinity targetting it would work because it would look for the nearest missile.
Vicinity targetting btw = the game automatically uses the weapon on the nearest applicable opponent from the cursor if it doesn't directly point at one.
I suppose weapons should default back to vicinity targetting if the direct target isnt applicable, or alternatively have the flak only function through vicinity targetting and completely ignore the direct target.
If it takes you two shots you arent using flak on par with your opponents.
That said i suppose there is no harm in having the dam from flak increased a bit so that you dont have to get a new flak cannon so frequently.