Apparently, it’s a thing in Tamriel to have books on their sides in bookshelves! There are some bookshelves that fit most books upright, or at least come close (the Alinor bookshelves, for example), but the only ones I am aware of that easily accommodate any books in the game are the large Apocrypha bookshelves and the built-in bookshelves in Kelesan’ruhn. The downside is that a ladder, stool, or levitation are needed to reach most of the shelves.