I guess it really depends on what one is arguing. For instance, you have people like Walter Block who believe life begins at conception but argue from evictionism anyway on property rights grounds. Nonetheless, he is still reasoning the unborn child as a human being. So I'd say he's a libertarian, albeit flawed on that point.
On the other hand, if you are arguing your pro-choice position from the perspective that unborn children aren't human, I could not consider you libertarian anymore than I could consider someone who believes black people or Jews aren't human to be libertarian. If the NAP doesn't apply to ALL humans its meaningless. Hey, maybe only cops and soldiers are "really" people