Can books be counted as books even if some points were used to cover points left in the hand and foot?
Yes. Your score at the end of a round is always 

+ points made in books

+ points from cards played (including cards in completed books)

- points left in hand

You can count all 3 separately and then add them together if you want. You don't actually need to remove cards for the negatives, but most people find it easier to pair up cards for the second and third and cancel them out.