Counter-spy turrets seem unable to destroy my cloaked ships. I have a group of 19 autocannon minipods sat right next to a counter-spy turret and despite receiving the message that my ships were being insta-killed the turret was missing every shot.
Interestingly, the turret chooses a different minipod as a target each time, after firing once at all the minipods the turret becomes inactive. If I save the game and reload it the turret ones again fires at each minipod in turn and then stops, without destroying any of them.
This is on 1.008, I've attached a save game, if you quickly swap to Povarra, the planet below my homeworld, you'll see the minipods.