@Hans-van-der-Tol I've been thinking about the same issue. Two alternative approaches could be:
use a small dot on the track in a different color rather than the large waypoint icon. Information like waypoint number could be shown own mouse over
if the map is zoomed out, only show waypoints with a custom icon or color and when you zoom in enough, also show other waypoints
And to make waypoints easy to find, you could make a specific waypoint visible if it is selected in the list of waypoints.