As we know, a-si thin film pv module has quite a different behavior from c-si pv modules. The pv efficiency depends on the sun irradation intensity and incident angle of the sun beam. We would like to know if HOMER can model these effects.

HOMER does not account for the effects that you mention.  It assumes that the efficiency of the PV array varies with the cell temperature, or if you choose not to model the effect of temperature it assumes a constant efficiency.