The icons are stored inside the Aperture Application package, in the folder
Contents > Resources
If you want the color back, copy all colored icons (all the tiff images inside this folder) from a previous Aperture version to this folder in the current Aperture version.
To reveal this folder, select the Aperture application in the Finder, cntl-click it, select "Show Package Contents".
But consider carefully, if you really want to patch the Application package. You have to be very careful, and you will have to do it over and over again, with each new update.