Are you talking about the carrier capital ship or the carrier cruiser ?
Most people have 3 or 4 carrier cap ships and 50 to 100 cruisers. Adding a couple of squadrons to the cap ship doesnt do much.
Its usually the cruisers people mod, and so adding 1 squadron to 100 crusier carriers adds a great deal of craft for the program to keep track of and display. Add 3 and suddenly your adding 300 extra entities to the combat. At that point, it can be a lag problem. (Been there, done that).
Adding 4 squadrons to the cap ship actually makes very little difference to combat mid to late game. But adding 1 extra to cruiser carriers makes a great deal of difference (unless you dont actually use them.).