Yes loot from pirates sounds good. Aliens are considered the worst bad event besides black holes and I see why you should not get loot from them. I think you should get loot from pirates though. Pirates are treasure hunters and it's natural for them to have some sort of treasure they found among their ships. Even if it's just a little loot it can make the expeditions more interesting.
I have always wondered why expedition battles never provide any loot. They have an infinite amount of ships but they never carry any resources. My suggestion is simple. Expedition battles against aliens or pirates should provide some type of loot. The amount of loot should scale with the difficulty of the alien or pirate battle.