It is explained in the anime that Hunter-nins are ninjas that hunts down missing-nins. Missing-nins are the people who betrayed the Leaf village and left. SO it is logical to say that hunter-nins would NOT stay in the leaf village because there is not missing-nins in the village, HENCE they are called missing-nins. Therefore, hunter-nins are outside the village hunting.

Edit: Just cuz we don't see them, doesn't mean they don't exist.