I would like to know whether this is more of a national convention, something specific to Google Maps or simply something done by the transport authority?
Red is not shopping area. Red is station undeground area together with all station exits. Still you can find some shops in thick part but rare. Especially it's impossible to find any shops in narrow red parts. You can check that info comparing map from Higashi Ginza station to Otemachi station through Ginza, Hibiya and Tokyo stations with this video. There are some shops but mostly it's just a passage way.
Dark red parts are pedestrian bridges over the ground overlapping underground ways. You can see them if switch to 3D view.
Yellow are major roads but it can be buggy in different zoom levels.
- Red: Underground shopping area
- Orange and yellow: see this Google blog Areas of interest