They are weak to ion damage, very easy to disable. You can get a hyperion with 3 ion pulser, blink behind and blast away, it completely shuts it off. Problem comes later.
the way i managed to defeat it was using the secret story ship plus an all laser paragon, and a monitor. yes, a monitor.
I kept at bay 1 of the 2 with the monitor and let the rest of the fleet deal with that one. Once it started splitting, i summoned some frigates (tempests and hyperions), to go around them and shoot them in the back, all while i kept the other one far away from the fleet.
Once everything was done, The fleet took care of the one i was keeping away.
In the end, i lost 3 tempests and a hyperion, secret ship was 1/4 hp, paragon still full hp, as with the star, the monitor