"Regardless of the legality of deleting the 1984 ebook, it's ridiculous to assert that Amazon should be able to destroy anyone's annotations for any reason. Those annotations belong to the user who created them."

The annotations were not destroyed. The work they referenced was removed. The claim is that, absent that work (with its particular page numbers , etc. I'm guessing) those notes are essentially useless, since they now refer to a void.