Can a merchant really find out who took the contents of my package?

I have ordered several items form online and the packages came to me by either fed ex,or ups and the contents were missing i called the merchant and they refunded me no problems but im wondering do they ever get there money back ?? or do they take a loss ? and also they said they would file a claim with the shipper but can they really deterime who took the items from the box ?? im just wondering if they just take the loss or do they insurance that protects them in situations like this