Yes, having a magnet levitate another magnet on a scale is no different then having both magnets on the scale itself. In fact its the same forces involved in either case (EM and gravity). What makes a scale possible is the electromagnetic force (largely electrostatic) between the scale pan and...
You can reduce magnetic flux with conventional shielding materials, like mu metal, but not stop them. However a superconductor will completely block magnetic flux lines as long as the field strength isn't too large.