Wild pirates are enabled, yes. Our only issue with those has been duplicating camps, no missing pieces in the camps yet. As in 2-7 identical camps spawned on top of eachother in the exact same place. I doubt its related to our issue though, seems very unlikely but annoying none the less as you take one wall down and there's another one at full health in the same spot. Easily fixed with a cheat kill command tho.
I'll try to pay closer attention if we play again, to see if we also see pirate camps with the same issue.
Atm though, we lost our motivation to play as we're randomly losing tons of resources every day.. up to multiple times a day, depending on how often we return to base.