If you paint the hat area of the rotor, including the area where the wheel mounts, you should regularly check lug torque. This is because the paint film under the wheel will fatigue with use, resulting in loss or reduction of torque on the lugs. This is why OEMs don't paint the portion of the hub where the wheel mounts. The exception is rotor plating, such as the Dacromet zinc-rich coating that some manufacturers use; in this case the whole rotor is usually plated.