To be honest, I'm not a huge fan of skill books as a mechanic. However...
I would really prefer a system like Neverwinter nights or similar where when your character gains a level you can choose to pick from a number of new spells or abilities. So you have trade offs to make and choices that allow you to make a unique 'ish character...
So, thinking outloud, I am probably saying ditch the classless system, or make it some thing people can unlock naturally.
...if this is the alternative to skill books, then skill books are
definitely the lesser of the two evils. Classlessness adds such a higher degree of customization than any form of class-based system ever could.
I honestly feel the best answer is for Larian to designate more guaranteed loot drops, such that at least one copy of every single spell is guaranteed. This doesn't necessarily need to be in the form of the skillbook directly; if clearing all the content guarantees blank skillbooks which can be Crafted with the appropriate scrolls, then that works too, assuming it's reasonable to assume the player has Crafting 5... so really, that would only apply to skills with a skill-level of at least 13. For everything higher than that, a guaranteed scroll hidden somewhere is fine; for everything lower than that, a guaranteed actual skillbook hidden somewhere is fine. It's okay to make some of these spots very obscure side areas, such as side quests. (If you need multiple copies of the skill because multiple characters in your party intend to use it, that would be on you.)