Board Thread:Theories and Speculation/@comment-28939725-20161201164545/@comment-734582-20161201225027

Susanoo is manifested by the eyes, but the true origin of the technique is in the brain. (even the mythology of Susanoo -that it was formed from the nose- suggests it's not a power actually tied to the eyes).

Since Nagato doesn't possess Madara's brain, he can't access it.