I can imagine that, although have never got anywhere remotely close to that number (my games tend to max out at a few dozen destroyers at most). Suspect with 2,000 I simply would not care in the slightest if any of my ships lost their repair drones, or even entire ships for that matter. Individual ships would be utterly unimportant to me when there are literally thousands of them. In which case I'd leave a repair drone toggle turned on permanently, not care if a ship lost it's drones, even if that lack of drones eventually killed the ship. To even get to the stage where I had that many I'd presumably be making them for free at my own shipyard, so conseqences for losses in battle would be completely irrelevant.
I do not however play the game that way. I don't build my own shipyards, make free ships, or own fleets anywhere near that order of magnitude. My ships matter a great deal for me, losing even a single destroyer is significant (thankfully has not happened for years). However that also means that there aren't so many of them that having manual control over their repair drones would be any sort of nightmare. Instead would be an absolute pleasure to be able to activate/deactivate repair drones with just a click on a single UI element (just as I do for defence or cargo drones), rather than having to use a clunky workaround with modded S ships & ware transfers.
So, not a nightmare in either case.