Yes, a control can be used to allow for differences in illumination. A single cell in the centre of the array can be used as a reference. If all cells are producing low power, then compare to some measure of the control cell to say if the array is shaded or they are actually performing poorly.
This isn't usually necessary as you can just take more measurements and apply some processing. For example, throw out any measurement when you think it might have been cloudy.
An irradiance sensor (a calibrated solar cell) can be used too.