From what I got so far, skills books aren't tagged as "read" when the Sim can't learn more from it - instead, they're tagged when they're, well, finished. Because my Sim has traits that make him read faster, I end up finishing books too fast.
So what happens when you finish reading a book in the game is that "rereading" is done way faster, and that comes in the way when you're trying to build up skills, mostly at levels 8, 9 and 10. My solution for that was to go on Options and toggle "Disable Autonomy for Selected Sim". That way your Sim will keep reading the book and building skill without stopping, so long as you keep them selected.