Once an antiaircraft gun has fired, I think all the tokens should be mixed up. Otherwise, if a miss is uncovered, any grounded aircraft can be safely attacked by flying over the miss space.
I think that is the idea behind that rule. If you want to try to seek a way through the Anti-aircraft protection, you must risk losing a plane to find out if it is safe or not. If you were allowed to reshuffle each time, I don't believe it would even be worth the effort to try to attack a base. Too much of a chance of losing planes.
Remember, that if a hit has been turned up, a plane is lost, and that hit is still there --- and the opponent still does not know a safe way through the AA defenses! That is protection enough. If a miss is turned up, the base will need to be aware of approaching enemy planes and better start to scramble its aircraft into the air to avoid being strafed.