Yes planes can pass over any zone that contain enemy ships, enemy planes, or enemy units. Planes cannot pass over neutral countries. In sbr’s they have to fight their way in if escorted or not if they are intercepted. After the interception or not then they get shot at by aaa and then if they survive that they get to bomb the factories and the tac bomber’s can bomb the airfields and naval bases. You are right that in the older version the aa was always active but not anymore. Hope this helps! :-)