Cosmic rays aren't EM radiation, they're very fast moving ions. The required shielding to stop cosmic rays and their secondaries is about 10 tons per square meter: a 33ft thickness of water or 100 miles of air. If they hit a superconductor, they'll only linger long enough to smash a path through the superconductor's molecules and won't care about the electromagnetic properties of a thin superconducting layer.