Is there any way to add additional information that can be viewed when the user hovers their mouse above the waypoint markers?
alternatively, is there a way to add custom markers by themselves to a map that has a route rendered on it?
This is unrelated to GraphHopper. If you are developing this for the browser you’ll have to use a toolkit like leaflet, openlayers or maplibre and read up on how to do that. (the code depends on the toolkit)
Or are you asking this for the JS client demo?