Madara destroys them. While he possibly doesn't have intel on Kakashi's Kamui, he could, when he sees him activating the Mangekyo Sharingan, send out clones to test with what powers he is confronted. This is a step which appears only logical if you fight unknown powers which could become dangerous, as he is on the other hand aware of the Mangekyo Sharingan itself and the powerful abilities it hides.