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This, which also works, is a simple edit of your code.

Code:
tell application "OmniGraffle Professional 5"
	set theDocument to front document
	set canvasCount to count of canvases of theDocument
	
	repeat with canvasNumber from 1 to canvasCount
		
		set oCanvas to canvas canvasNumber of theDocument
		set lyrNotes to layer "Notes" of oCanvas
		set blnVisible to visible of lyrNotes
		set visible of lyrNotes to not blnVisible
	end repeat
end tell