If you start an application, such as Nautilus or Gparted as sudo or root and it has the default GTK theme, here is a solution: simply run the following commands:
sudo ln -s ~/.themes /root/.themes
sudo ln -s ~/.icons /root/.icons
sudo ln -s ~/.fonts /root/.fonts
This will create a symbolic link for your themes, icons and fonts in the root folder for the respective folders and will allow the root applications to to use the theme that you have set.