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It doesn't keep the stencils in that folder any longer. The new location is at ~/Library/Application Support/The Omni Group/OmniGraffle/Stencils.

Also, I don't believe the stencil folders are actual file system folders. You can make new folders in your stencil list by selecting New Favorite Stencil Folder from the gear menu in the stencil window, and just drag your new stencils in there after installing by double-clicking.