You can get transparent holes by setting the fill to none on the pad and creating a hole in the underlying path, but AFAIK Fritzing will replace the center of the pad with green if connected or red if not connected so it won’t appear transparent in Fritzing. You can change the color in preferences and thus could change it to white (you don’t appear to be able to set none) which may do what you want at the cost of not knowing if the pin is connected or not. The connect color is added by the Fritzing code so occurs after the svg is loaded (I assume by modifying the fill value in the svg on the fly.)
It is the connected or not connected state that changes the color of the pad. For female pads by default (I think when unconnected) they are transparent but once connected they go green (even if the connection is to another member of the bus that they are in.)
Peter