I think nz in the CMAQ run script is used only for convenience, as a portion of file names. CMAQ determines the number of model layers from the meteorological input data from MCIP.
MCIP can be used to collapse vertical layers, so that there are fewer layers in the MCIP outputs than were present in the original WRF data. This practice is not recommended, and is not typically used at EPA, but I am not aware of any studies that have investigated impacts of layer collapsing.
CMAQ should be able to handle gridded emissions that have fewer layers than are in the model. In recent practice, gridded emissions typically have only one layer, while vertical distribution of point source emissions is calculated using a plume rise algorithm.