Should the weight of the lifting surfaces be deducted from the weight used to calculate the C of G of the aircraft?
The center of gravity is relevant for all inertial forces. For example, if you turn, the centrifugal force would be calculated with the mass of all aircraft parts, including wings and rotor blades.

If you want to calculate the loads on the aircraft structure, things depend on the location. If, for example, you want to know the load on the wing root or the helicopter rotor shaft, you use the total mass minus wing / rotor mass times the acceleration to calculate the force.

While there are cases where the wing mass needs to be subtracted, center of gravity calculations must include it.