He wasn't using Rikudou Chakra. His Chidori wasn't black and his Susano'o didn't get the marks that come with using Senjutsu on it.U really are an idiot who thinks himself to be too smart. Sasuke has rikudou chakra due to which his attacks work against Naruto. Even Kakashi's chidori worked against Kaguya after he got Rikudou's chakra from Obito.
So its not that Naruto doesn't have omyondon (he does since everyone having the senjustu of six paths have shown omyoundon......Obito earlier could use it but after awakening rikudou senjutsu could use it.......we even got the confirmation through Sasuke that Naruto's gudoudamas are the same as Kaguya with the only difference being that they are smaller)....but Sasuke has Rikudou chakra. U_U
The ability to negate Ninjutsu comes with taming the Juubi, Naruto doesnt have the Juubi so it's impossible for him to have the negating powers