Rumor has it that Polish ebook publishers do exactly that.
In Poland, there's no single E Ink reader company, so there's no DRM standard that would be compatible with all devices that you might want to read your books on. As a consequence, offering unprotected epub files is standard practice here, but all kinds of watermarks, from divs that are 1px by 1px, to subtle modifications of your book's cover, are pretty common.
You can beat this kind of watermark pretty easily by getting three copies of the book and comparing them with diff. You need 3, not 2, so that you know which variant is the original when you notice a difference.