On sins of a solar empire can pirate bases be captured

yes you can..it will be its own planet thing in which you can build up You can also upgrade it's defenses, with multiple turrets or even a superweapon, and it has a bonus on gold. But it doesn't actually have any populations since in the logistics will only have one upgrade. I'm not sure yet if this can be overcome with the economic research of the TEC, but with the Advent and Vasari, it will only be limited to one.