So basically, you've got 50 or so (can be changed in options menu) of the ships in battle at any one time, and a reserve of ships that is just a number. When a ship is destroyed, the debris is removed and a ship is drawn from reserve to take its place in a different part of the formation (Position of reserve drones is tracked based on speed and heading of the orbit, but they don't move until drawn into play). For handling nukes and frags, 20 or so of those ships could be placed far away in various parts of the formation. If one of them is destroyed by a nuke, every equidistant or closer ship is destroyed from the reserve. I'm not quite sure how to handle frags, for unarmored drones it can just be considered dead if a lot of fragmentation passes through but armor can't be simulated without bringing on lag issues, armored drones generally aren't used more than 100-200 at a time so it's maybe not that big of an issue. When the drones get into range, the damage done by the drones in play is used to judge how much the reserve drones within range would be doing. This would sacrifice a lot of fidelity, but I think not being able to use mini drone swarms at all is less realistic than abstracting the swarm. We also might need to make a way for drones to get drawn into reserve during the same instance, some people bring their carriers into combat or just like watching the drones launch.
As a counter-idea to achieve the same end, why not have swarms group? I can't say I'm a fan of replenishing swarm losses from thin air, it doesn't strictly follow reality.
Say, 5 missiles could be grouped "in formation" and calculations performed on the group as a whole.
An extension of that idea would require munitions to wait after being released to form a group, which doesn't seem too impractical with rapid fire micromissiles.
Manuevering shouldn't present any issues as they'd all act together. Final impact and damage results would have to be on an individual basis to avoid over generalizing the effect of a swarm. CIWS damage might have to be applied solely to one item in the group at a time.