I understand what you´re trying to do with this rule but I find it to be way to much hassle and slows the game down too much, this would indeed be a housekeeping nightmare. Personaly I find the ordinance rules to be fine, they work. However I will share two brainstorming suggestions I came up with.
suggestion 1) Change ordinance limit rules:
Ordinance limit = " at the end of your ordinance phase, remove all enemy attack-craft markers not on CAP"
This would limit the range of bombers to 40 cm. If it goes too far you could simply INCREASE the speed of ordinance by a %. One could also limit torpedoes this way.
Suggestion 2) Change the the "reload ordinance" order and ordinance limit rules:
reload ordinance = "makes it possible for the ship to fire ordinance this turn OR maintains attack-craft markers already on the battle equal to launch capacity.
Ordinance Limit = "at the end of your start phase remove all friendly attack-craft markers not supported by capitol ships".
Not too sure about the wording but let me explain how this would work with an example: 2 dictators launch their attack craft, 2 fighters on CAP 2 fighters and 4 bombers in 2 waves. Their next turn comes along and only one of the dictators passes a reload ordinance. 6 of the 8 attack craft markers are not on CAP and 2 of them need to be removed from either of the waves (or 1 each).
This would not limit the range of Carriers but it would limit their long range firepower some of the time. Again one could do this with torpedoes as well.
suggestion 3) (comedy suggestion)
I hate this one because of annoying marker spam, but whatever
Ordinance limit = "at the end of your ordinance phase, remove all enemy attack-craft with fuel markers on them. THEN put a fuel marker on all enemy attack-craft not on CAP"
Comes closest to your initial suggestion.
Personaly I like the suggestion that fracas made about just limiting the range of attack-craft from any ship with launch bays. Cleanest and simplest solution. Does not have to be 60 cm tho, could be 40 or 120 or whatever.