1) Luddic Path bases and cells continue to spawn even after their entire faction has been destroyed.
2) If you capture a world that is planning on sending a fleet to attack one of your planets, the fleet will still spawn - only now it will claim to be one of your fleets. This would be fine except that they will still carry out their original mission to bombard/raid/strike your planet, and since they're now technically friendly none of your defenses will even try to resist them. There is literally no way for the player to stop such a fleet once it spawns (the best you can hope for is that pirates will take them out first, which is very unlikely).
3) With regular empires, one can whittle down their defenses before attacking their defense stations. By that I mean you can hijack satellites to lure their fleets away, then ambush the fleets, and then finally take on the station once they've all been cleared out. This is possible because it takes time for them to spawn more defense fleets. This is not true of spawned pirate bases and Luddic Path cells (Admantium raiders as well if that Archean Order is being used). In these cases, the second one fleet is destroyed another instantly spawns from the station. This can go on forever, by the the way. This ends up turning attacks on these "minor" bases into a Herculean task that makes star fortresses look easy in comparison.