Make hangars damageable and repairable just like engines. While they're disabled, they stop replacing and rearming. They should also benefit from Automated Repair Unit and skills which make engine repairs faster.
This requires fighter bays to have a definitive single location on a ship's hull. Currently in-game, a single fighter bay can have multiple "launch ports" anywhere on the ship's hull, and it doesn't make sense that if just one of those is hit hard enough the whole bay gets taken out, since that very much depends on the way the ship is laid out.
For a ship with an especially large flight deck area - say, the Astral - where do you determine is the point damage needs to occur at to hurt the nanoforges? Obviously you can't just make it a wide area, that would be ridiculous and wholly unfair to those big carriers, since if they're taking general fire like that they're probably already screwed enough.
While I like the idea in a vacuum, this is something that will be confusing for combat carriers and just plain cruel to dedicated carriers. Yes, I know carriers and fighters are very strong right now, but I'm not convinced this is the best way to help that.
At the very least, perhaps instead of "disabling" nanoforges, damage taken near a fighter launch port could merely incur an immediate penalty to the fighter replacement rate (like, 1-3% based on damage taken). That might still be overcomplicated, but I think would have a better result.