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.
![Tongue](/smf/Smileys/default/tongue.gif)
Anyway, as others said they can safely be deleted. There's nothing in them so they're of no use anyhow.