Hi Nicholas,
SAM's Detailed Photovoltaic model does not model individual cells, so it doesn't distinguish between modules with full and half cells. The shading models either model shading as a reduction in the beam irradiance over the entire array, or for self-shading, make some assumptions about the layout of cells in the module based on a conventional full cell module with three blocking diodes.
The "CEC Module Model with User Entered Parameters" option uses the number of cells in series in the numerical solution to calculate an I-V curve from module parameters. (It uses the value to determine initial guess values for the solution.) If you use that option to enter parameters for a module with half cells, I have found that the solver works best if you use the number of whole cells for the "Number of cells in series" input, so for a module with 144 half cells, you would enter 72 as the number of cells.
Best regards,
Paul.