Is there a format games can be in that allows them to be used both by Wii and Dolphin but doesn't keep all the dummy space?
Set up the NTFS partition as sparse. The files will still be the same size, but sparse partitions will automatically compress the space used by the dummy data, so you can fit more on. Cfg is able to write to sparse NTFS partitions too, although I'm not sure about CleanRip.