To get much of the drone functionality back, install Converted Hangar and a Claw wing. Claws zap enemies at least as well as drones did, although they do not give more shot range. Admittedly, more shot range was the more important power of the drones.
Without more shot range, Apogee was hit hard. It has neither the range nor the speed to fight effectively in the new cowardly AI metagame. (Well, it has beams for range, but without kinetics to back them up, its low beam firepower is hard countered by most shields.) If that should be fixed, I recommend changing the heavy hardpoint (only) to a universal or hybrid. Why? Apogee and Remnant's Brilliant cruiser are similar in design - both have awkward mounts, both have 0.6 shields, both have Active Flare systems to compensate for terrible PD (due to awkward mounts), both are relatively slow. Apogee has extra hauling capacity, while Brilliant has a builtin flight deck. Brilliant is an excellent sniper, while Apogee cannot do much in a fight on its own. The easiest way to give Apogee some more range is to let it mount some ballisitics, like Mjolnir or Gauss Cannon.