To my knowledge there is no limit to the # of .mod files you can stick in a single folder. At least not any that I've found. Brezgonne puts all of his Tholian models (way more than 6) in a single folder and it works fine.
As far as the model.siz file goes, as long as you have the correct path to the file, and the folder is in the "models" folder that the model.siz file is in, it'll be fine.