A Boeing built 747 freighter (not a converted aircraft) does not have main deck cabin window openings (holes). It uses different skin panels to those used on a pax aircraft. Also it only has openings for 2 main deck doors thus the reinforcing that goes around the windows and the "missing" 8 doors openings is unnecessary.
On converted freighters you can leave the cabin windows installed or replace them with metal plugs (customer choice). The unused doors are simply locked closed and placarded accordingly.
I do not know enough about other freight aircraft to comment on them.