They don't take a whole lot to destroy, if you have decent missile tech you could design an anti-FAC missile cruiser with fast, maneuverable missiles (try and get the 10k speed hit rate up high) and low res fire control/sensor so you can target them from a ways off. A couple size 9 warheads should do the trick.
The worst part is the micromanagement of targeting all of them with a couple missiles each. You could design the missiles with sensors and just fire a whole bunch of small volleys (each volley impacts together, so if you fire a big volley it only kills one ship) and let them find their own target after the initial one gets destroyed. Just figure out how many of your missiles it takes to kill one and assign that many launchers to each fire control and set all the fire controls on a target and fire away. Just make sure the sensors have longer range than the missiles and enemy ships would travel in 5 seconds (so missile speed + enemy ship speed both multiplied by 5 = minimum sensor range, just to make sure they don't zip past eachother without the sensors detecting them).
They wouldn't need to be super long range, just enough for you to be able to fire a whole bunch and let them take care of the swarm on approach. Something like 10m km would probably be plenty, with sensors tuned for 800 tons. Even with pretty low end techs (like tier 4 stuff, the ones that cost 8k in missile research, engine one is a bit more expensive of a prereq) you can make something that has 10m km range, size 9 warhead, with a 90% hit rate vs 10k speed in a size 8 missile. Similar launcher techs would fire them every 60 seconds. Design a ship with say 12 launchers and 3 fire controls and enough magazine capacity to carry about 240 missiles then build yourself 10 of them. Most of em would probably go down from a volley of that, so that would take down about 30 ships every 60 seconds. Even just sitting still at 10m km you'd have time to fire 17 of those volleys before they got to you. Flying away from them at just 2k km/s would let you fire all 20 of your missile volleys before they got to you with time to spare. 20 volleys from 10 ships like that would destroy four or five hundred FACs for sure, maybe six hundred.
I've never seen that many swarm ships. Worst I've had was about 100 after an NPR had been feeding them scout ships, and a similar tactic worked fine on them (although I didn't need as many ships).