Yes. HOMER Pro assumes the system does include a maximum power point tracker (MPPT). HOMER Pro uses a very simple model for the PV array output: it assumes the power output of the array is linearly related to the amount of solar radiation striking it. (For details, please see the article on how HOMER Pro calculates the output of the PV array.) That assumption is fairly accurate if the PV array is equipped with a MPPT, and not very accurate otherwise. So HOMER will model your system better if your PV array is equipped with a MPPT.

When you specify the properties of the PV array you need to account for the efficiency of the MPPT. You can do that using the derating factor.