Pirates are disabled in server config ("ENEMY_SPAWNING = false //Enables enemy spawing"), however, about 30 pirates spawned on me, several sectors away from any pirate station. I spawned some trading ships to buy me some time while I found the command to wipe mobs, then managed to wipe them a bit later.
If you want to replicate it, you should just be able to drop the config file into a server's config - my server is always up-to-date, and this has been pretty consistent for some time (though this is the first time it's spawned more than 1 or 2).
Server is run from the launcher on the site, and client is run from steam, but I doubt that matters.
On a related note, is there a way to restore missing blocks to a ship yet? (If so, by admin command? If not, is there a way to rollback to a previous autosave?)
I've attached the log file in case it's useful.{F4770}