to answer your question about skill books and mutations, yes if you use books and then mutations you lose the effects of the books you spent. thankfully they have a way to lock your skills, so if you use books and don't want to lose them you can lock them and they cannot change. Also you are able to use mutations first and then books which allows you a chance to not need to spend the books at all, but if you don't get the skills you want you still have books to spend.

Books in later versions are easier to get than we have currently, I wouldn't worry about wasting books at all as you will likely get duplicates of the books you want anyway, so it's just a matter of playing smart.