You are close, I think you just want to change your output filenames to look like:
So if your layer was "ocean" it would end up like "c:\data\DNCs\DNC12\A\ocean.shp". The one piece that is missing is the changing of the path tree. You can't currently do that, but I think I could add support for some kind of output path replace string, like PATH_REPLACE="DNCs=SHPs" or something like that to replace one string in your path with another. Would that work?
Global Mapper Guru