What is the allowable stress due to Harmonic loads? I realised that CAESAR II considered the harmonic load case as "Occasional" but in reality it is with high fatigue cycle. Is it correct that the allowable stress supposed to be compared with endurarance limit of material for the harmonic case? or use S-N curve?

If you provide an S-N curve in the (static) model input and specify the number of expected harmonic cycles in the dynamic input, CAESAR II will perform a fatigue evaluation in place of that check as an occasional stress.