According to the blog, the bonuses from fleetwide skills like that decrease after the fleet exceeds some threshold, such as the six fighter bays. It does not seem unskilled characters will take penalties for having too many carriers, just those that have skills to discourage "mono-fleets".
I'll have to reread it I don't remember all the details. I don't think I caught that the first time I read the blog. I guess I can take some consolation in the idea that skills will most likely be heavily moddable so I can likely increase the threshold number.
Back to possible solutions:
If going the nerf fighters route, based on my experience I would agree with Schwartz: changing PD requires a rebalance of missiles too. That might get pretty involved before all is said and done. Would reducing fighter defenses (and thereby increasing PD effectiveness that way) be out of the question? What do we think is the threshold of that kind of health/armor reduction before fighters themselves become unattractive?
Radical solution:
Turn fighters into mere recievers of the carrier's energy. Flux generation is proportional to a normal weapon rate and a distance-from-carrier based multiplier.
In concept, I like this idea because it's a "tried and true" balancing mechanism for any sort of weapon, including fighters. If this were the route taken, I would recommend flux be generated each fighter replacement that scales with replacement rate increasing that amount as more and more fighters die. Each fighter entry would have its own flux cost per replacement in the wings csv file. Max flux carriers stop replacing all together until they vent?
However, this might be a lot of work. I'm not sure. It also might run the risk of overly promoting weaponless carriers, which would feel a little off. And venting is fast enough that it might not even matter since fighters have such a large range... hmm second guessing it now. While good in principle it seems like there might be a lot of complications. Not saying it couldn't work though.
*EDIT*
I think the primary issue with fighter swarms is that PD is just not that effective against them. PD is geared toward missile defense rather than swatting fighters and it shows. If you're going to add an arbitrary mechanic to dissuade mass fighter attacks, increase the effectiveness of PD against fighter hulls and make them take losses. As has been said, granular control over individual fighters isn't possible but an attacking player could be warned that condensing a ball of fighters onto a single target makes them more vulnerable to anti-fighter weaponry.
I don't know what that looks like, per se, but the chief mechanic for fighting carriers is depleting its replacement rate. I feel it's better to lean into this mechanic than anything else.
I agree with the last part about replacement rate. Even if you could effectively warn the player, though, since they don't actually have that much control over what AI fighters do, I think that warning will in reality only translate to: "Don't give fighter strike orders or fighters will get worse and hope that the AI doesn't do it for you"