The bonus of getting free skill ups is hard to pass up for all you're doing is clicking it then move on. My first few characters I would click bookshelves immediately upon seeing them whenever I came across them in towns, dungeons, and through quest zones that you'll never see again. Then the realization kicks in, the same bookshelves appear in VR1 and VR6 as they do in your starting zone and it continues down that trend all the way in every progressive zone. Regardless of when you click the bookshelf when it gives a skill up, it doesn't matter if the skill is at rank 5 or rank 49 you'll get the skill up.
Lately I been skipping every bookshelf on my recent alts, will probably wait until VR1 to start clicking them. I don't have to backtrack to get them either, the same ones will appear in the next 5 VR zones and again in the next 5 as well. I figure if you skip all the bookshelves until you reach Cold Harbour you can maximize the use of bookshelves to get those last few points in especially if you're an all around crafter. Why waste them on low level skills when I can use them on building the more progressive stuff later on?