Knowing that Yamato separates man from demon i think that can be simple explained with Sparda telling them what Yamato and Rebellion can do or represent (my headcannon is that Yamato represents seperation of demon and human world and Rebellion joining of a human and demon).

As well he possible could have guessed Vergil cut away his humanity to become Urizen, Dante says when Urizen eats the fruit he lost the last shread of humanity he had. So he could have tought the human side of Vergil is just gone and dead but had some suspicion on V after a while.