Except....

I am assuming that the carrier is attacking
or defending something. A fleet, station, or planet.

That target can signal the carriers position to the
cruiser in hyperspace. With accurate Minbari jump engines they can get close enough to slice it up before it can escape. You lose a big chunk of your fighter complement when you lose the carrier.

Now...one way around it would be to have the carrier (or another ship) hold open a jump point and have the fighters enter through it. The carrier hides in hyperspace till the battle is over. Picks up the fighters afterward. Only problem is that you better win the battle or you can never pick up your fighters.

The whole "pure" carrier concept as we know it today relies on being able to detect, track, and attack a target before it can do the same. Hyperspace makes that extremly difficult.

As well as being a wonderful dramatic tool.