I've never been able to prove it, but I believe that deleting custom content in the game causes empty packages. I've always noticed them after I do that and other times I'll go months without ever getting them but then I delete stuff in the game and there they are again.
Maybe the game leaves a residual file when you delete something in the game, but it also seems to delete the wrong files at times too. I once had the white recolor of Windkeeper's Good Luck Cat end up an empty package and I know I never attempted to delete that in or out of the game, so it seems like random files just get shredded sometimes. Fun.
Anyway, as others said they can safely be deleted. There's nothing in them so they're of no use anyhow.