Once 1 CBT gets destroyed nagato can simply create another one. Naruto spamming his clones will severely diminish his chakra and they would be next to useless against nagato's techniques. Shinra tensei blows back any clones that get too close, but as i said they wont even be able to find him in his chameleon. And if it ever gets too overwhelming then nagato can use chou shinra tensei as a last resort, or even better he can use the gedo statue to completely wipe out naruto's soul in an instant..This is just a last resort though, Nagato would never need to use it because preta, human, asura, and deva path are more than enough to take him