I'd say it counts as one book, if you'd simply break it up after NaNoWriMo. Of course, it all depends on the connection between the two books. If it's broken into parts like the Lord of the Rings trilogy, then it'd surely count as one book for the NaNoWriMo (you can easily imagine all three books together in a chubby novel).

As for myself, I know that my novel - be it finished through November or sometimes later - is too big for a single book. I'll see what I can do about it, but I'm not going to touch/edit it until after NaNoWriMo.