Yes, the pilot would certainly notice the difference.
When the engine applies clockwise torque to the main rotor, the body of the helicopter experiences counterclockwise torque. When the pilot increases collective to increase the amount of lift the main rotor produces, the engine will need to apply more torque to overcome the rotor's increase in drag. Therefore the pilot would have to apply right pedal to prevent the torque from turning the nose of the helicopter left.
If the rotor turned counterclockwise instead, these directions would be inverted. So if the pilot was flying the helicopter with the assumption that the main rotor turns in the opposite direction that it really does, he would tend to apply the wrong pedal and the helicopter would start yawing.