One possibility to balance that is to make the ship much more detectable, via any mechanics in place.
Also what @Naiba suggested. Simply make the shields a slightly more aerodynamic shape than the ship they are protecting.
You could add a mechanic to allow players to make shields slightly more ‘extended’ to make for a more aerodynamic shape, at the expense of a larger hitbox and lower strength. It would make the ship slower, but more maneuverable. Perhaps have a toggle-able on/off system that allows for the ship to automatically change the values based on what the pilot is trying to do or have a micromanaging system.
Not a huge advantage, but enough so that an experienced player will know how to exploit these to make a corvette slightly more effective than a brick.
I would, however, wait until adding an effective anti-fighter/bomber weapon systems before fleshing the system out. Because the only ship that would really benefit the most from having more maneuverability in an atmosphere would be the corvette, and that only really would be useful when combating interceptors and bombers.
(four people posted while I was typing lol)