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There are two things going on here:
  1. Lion hides the Library folder
  2. Omni has changed the location of the OmniGraffle support files

I'm not yet a Lion user, but I understand that if you hold down the option key while clicking on the Finder's Go menu, the Library will appear as an option.

As of OG 5.3, the support files are in a slightly different location. Here's the relevant snippet from the release notes:

The shared support folder for custom OmniGraffle stencils, diagram styles, templates, and shapes has moved to $HOME/Library/Application Support/The Omni Group/OmniGraffle to conform with Mac App Store guidelines.

So after you go to the Library folder, you'll drill down into Application Support, The Omni Group, OmniGraffle, and there you'll find the Templates folder (the Scripts and Stencils folders also live there, of course).