It's a different methodology for sales is the most likely answer, and I doubt it costs the book store "nothing". In all likelihood it's probably more like... Book store purchases X number of copies of a book up front and puts them on sale. Eventually they decide that 5 copies will never sell, and so they destroy and return to publisher (this is an important distinction - Any friend of mine who worked for a book store, they had to remove the front or back cover of the book/magazine/whatever before return) and are given a credit towards future orders rather than a refund. That book/magazine/whatever is then recycled by the publisher in bulk, for which I'm sure they get a credit/tax break/whatever.
There's likely much less of an avenue for Best Buy/Target/Amazon/Etc to return unsold copies for any kind of credit, because at that point what is the publisher/distributor supposed to do with those copies? Re-sell them at a lower cost to other retailers? What's the incentive there? They could just as well refuse to accept the return and keep the money they already received from the retailer, who then has to sell the product at a loss or otherwise trash it (for instance I know Target "donates" a lot of items to Goodwill - which they can then write off for taxes)