This isn't an actual problem Amazon has, and Amazon has enough problems that we don't need to make up new ones to discuss. Used items are tracked and sold individually (with their unique condition described and viewable by the purchaser), unlike new items. They're not just binned together by condition, when you buy used you're buying a specific item out of inventory. A "new item missing packaging" would not be sold as a new item. "New" items that are returned to Amazon are re-sold as used under the Amazon Warehouse Deals brand, even if the packaging looks factory sealed, for example.
And what about "New" items missing packaging etc.?