[Joel]

Another interesting by-product of the Sandboxed environment is that those Stencils and Templates that come 'bundled' with OmniGraffle 6 are written out to the Container, instead of being read from within the application's file wrapper.

That means that if you have no need for any resources that come with the application, feel free to move them to the Trash via the Resource Browser, or you can also show them in the Finder from that interface and manually move them to the Trash.