Ok I don't know if this has already been posted, but I seen on at least several different occasions that the Pirates have been killed off by AIs using only culture to do it, not the Advent superweapon, just the general Culture spread effect.
It's pretty much like how a player uses their culture to flip a AI planet into a netral planet, but from some reason this only happens with AI culture, never with an actual players culture effect.
In one weird case when playing the Systems Of War map against 3 hard setting AIs, I'd had seen the pirate faction killed off at about 6 to 7 hour mark in the game, so low and behold my surprise when I decide to kick whatever AI had take the pirate base from it. I jump into system with a lvl8 titan (to act as a damage soak) and 9x lvl10 capital ships (Mainly carriers to deliver mass strikecraft attack) to find 600+ pirate ship and completely untouched defensive structures. Needless to say I sacrificed the titan and and just manage to retreat about 2/3 of my capital ships.
This is definitely a bug, and no superweapon had been used to that point in the game as I'd taken all the outer Star Systems before hitting the larger central Star System and I'd had been using hit and run strikes to destroy superweapon shortly after they started building them.
In the screen caps shown I'm playing TEC Rebels with the research tech to make you neutral/ally to the pirate faction, just show what I'm talking about. And the map is Areolian Sector from the Large maps. the Game version is 1.02.
I only just DL'd the 1.03 patch 3 hours ago and haven't yet played a long enough game to see if this bug has been addressed in the patch. But from the patch notes, I'd say it hasn't.