The narrator doesn't tell us what Nathan Radley knows, but I suspect he's aware of what has been going on with the children and their games. He wants to scare them away completely, so he shoots over their heads. He figures this will put a stop to the curiosity the kids have about the Radley house and wanting to see Boo Radley. He knows the gunshots in the middle of the night will bring the neighborhood out, and the children's antics will be exposed. Nathan knows Atticus will put a stop to the children's interest in Boo.
Mr. Radley thinks he's shooting at a Negro who got so scared he turned white. Or is that who Miss Stephane think he's shooting at?