I really like your style. It reminds me of the style Le Guin use in Earthsea books for pictures and maps. A thought on the sites, it would depend on if you could group them some way you could use that to name them. For example if they are all hazards you could name them dangers and mark them with a tiny skull. If they are all just significant location you could just label them as Noteworthy and keep the x. This sound like some pompous fictional academic to me but it fits how artistic the map is.
Over all I think the map is quite beautiful.