Well i found it always a bit silly that a shot Pirate Station becomes scrap rather then normal blocks. A shot ship doesn't turn into scrap either. If the default pirate stations were to be made up of simple blocks then it would not be an issue if people started farming them. My Home Base is mostly rock and lamari. The pirate stations could also be made up of asteroid blocks rather then expensive armor.
And the Loot Chest like Lukwan says really needs a come back. Since right now Pirate Stations are mostly ignored.