There is no correlation between the organization of your referenced folder tree and the organization of your Aperture Library. Aperture simply knows where referenced files live in your folder tree. You can make all the changes you want to your Library organization. That will have no impact on the organization of your referenced folder tree. Changes you make to your Library organization will not cause changes to your referenced folder tree.

If, however, you move a file or folder in your referenced folder tree, you will have to open your Aperture Library and tell Aperture where you moved it to via the Locate Referenced Files menu option.