The way I understand it is that once this is implemented, duplicate hats you already have will be deleted, just like how duplicate illusions were.
Unless Fatshark changes something, then you will probably still be able to get hats you already have from Commendation Chests. But since you already have them, you’ll not actually get anything.
If so, then every 50 chest or so you would lose out on 1 item. Not a big deal in my eyes, but it would be nice if you stopped getting hat drops when you have them all.