After thinking about this some more beyond the knee-jerk response I posted earlier, I realized that when shopping for ebooks (or library ebooks) I am usually shopping by category, so I already know the books I'm browsing are books I'm likely to be interested in. Therefore, I barely notice the covers.
However, if I were wandering among a display of paper books, I would notice the cover. Usually, covers convey something about the type of book. If the cover shows a couple in a passionate embrace, it's a romance; if the covers shows a picture of a gun, it's a mystery/thriller; etc. So if I saw an anime-style cover, I would likely assume the story was anime and pass it by.