Kind of similar to another suggestion, but rather than or in addition to including a new command to retrieve loot, how about including it in the current commands?
Attack enemy / patrol could include logic so that once their target / all enemies are dead, they swoop back around and pick up any eligible loot prior to ending / returning to the command.
Salvage could natively also include loot collection of eligible pieces. (As of current, it seems like a ship set to salvage will only collect loot that is dropped as a part of the salvaging process and will ignore anything that dropped as a part of the process that created the salvage in the first place.)