[Andrew N]

OK I have an answer. OG great support provided this script:

tell application "OmniGraffle Professional 5"
	set theDocument to front document
	set allCanvases to canvases of theDocument
	repeat with canvasCount from 1 to (length of allCanvases)
		set nextCanvas to item canvasCount of allCanvases
		set nextCanvasLayers to layers of nextCanvas
		repeat with layercount from 1 to (length of nextCanvasLayers)
			set nextLayer to item layercount of nextCanvasLayers
			if (name of nextLayer is "Notes") then
				set currentVisibility to visible of nextLayer
				set visible of nextLayer to not currentVisibility
			end if
		end repeat
	end repeat
end tell

Seems to work a treat. More complex than I thought...