In Episode 472 of Naruto Shippuden, Kaguya and Black Zetsu thought Naruto with Truth Seeking Orbs surrounding was the original among the clones, but it turned out to be a clone once Kaguya struck him with one of her black Rods.
Why couldn't Kaguya use her Byakugan to see the original Naruto? Byakugan can see the real ones among clones and I don't think anyone has a stronger Byakugan than Kaguya, right?
And if Naruto had Nature Energy and couldn't be seen- so does Kaguya, she can merge into nature and kill enemies by merging into nature as per Epsiode 470, when she teleports everyone into Ice World and turns into Nature Energy and traps Naruto under icicles.