If they get the same book to scan twice, why actually do the second scan? Why not just use the scan from the first copy of the book? And if that is the case, now they have a fresh copy of the book with its spine intact.
It would be a waste of the resources invested in the production of that physical book to not find some productive use for that copy.
Besides the possible copyright infringement problems mentioned elsewhere on this page, I occasionally write notes in my books. If I sent them an older book with a bunch of notes in it and got back a PDF that didn't have those notes, I'd be upset.
A potential compromise, if simply giving out the same PDF is legal, is them offering a big option saying "Our records indicate we have this book on file! Do you want us to immediately send you a PDF copy when we receive your book [potentially discounted pricing or even a percentage of resell profits], or would you like to wait for a scan?" So yeah, now they have to do something with the hard copies, either resell or donate.
Edit: No need to speculate, they claim to shred and recycle everything after processing.
Some people write notes on the margins of the page and underline key-phrases when reading. I don't think they would check each book to see if it was "clean".