When is it safe to sell books and contracts?

I did trash many books and notes on my first playthrough, and I didn't notice any case where I needed something later. As you said, you should read them all beforehand as they might trigger quest advances or give you bestiary entries.

One item I'd be careful is the pass to get across the Pontar, it looks similar to other notes and you might want to keep it.

You could also restrict selling books and notes to one particular merchant, that way it is easier to buy something back if you actually need to.