Be aware that the replacement rate ticks down while rearming fighters, so even on recall mode a constantly launching carrier will quickly grind to a halt.
Have you ever used Astrals?
If it doesn't lose any wing it doesn't need the replacement rate at first place.
Even if it does lose a few, a brief regroup after recall is enough to make it back up to 90+.
I'm using an Astral and I can confirm that. When spamming Recall Device, you essentially remove replacement rate drop from re-arming bombers. But that's okay - it's this ship's gimmick. Without it, it would be pretty underpowered.
What I tried to state is discourage making frontline mobile infinite missile spaming platform.
Especially longbows, they got very good range so they can stay intact and keep spamming sabots on your face and you don't have other ways to stop it except overload/kill carrier itself while other ships are possibly stopped by emp arc or claw/terminator drone flanking the unshielded area.
I'd say there's no point here. You already have to get in range to shoot the carriers in order to deliver the EMP damage. So it's not going to help against Longbows' range, as you cannot deal EMP at range higher than that of Ion Beam or Tachyon Lance (unless we're talking fighting fire with fire, i.e. your own sabots).
Also, keep in mind that most carriers are slow and can directly attack only one ship at a time. I've actually exploited this property when attempting to capture my first Astral in current save. If you attack it at once from multiple sides, it's in trouble, especially when you use other friendly ships as a distraction. I know what I'm saying - RNG hated me and I had to fight that Astral multiple times before I got to recover it, and the most powerful ship I had was an undergeared Oddysey.
Anyways, if in the above situation the flight decks could be disabled by EMP, the fight would imo be a joke. A carrier would never survive a single direct assault. They are already very vulnerable when their bombers get destroyed, due to replacement times. Even in the Astral, you have to wait a little with fighters set to Regroup when too many of them get destroyed and it takes
minutes before you get your fighters rebuilt if your replacement rate gets too low - at which time you can also receive a direct attack from the opponent. Having the flight decks disabled in this situation would extend that vulnerability severely.
Like I said, it seems logical at a glance, but it's a pointless nerf. And not everything that seems logical should be part of the game.