In version 1.6 waypoint data was made local and there is no "proper" way to set or remove a waypoint.
only removes the client side visual effect of the waypoint and in certain instances the game will recreate & display the unwanted waypoint.
I posted about this
http://www.esoui.com/forums/showthread.php?t=4366 when 1.6 was on PTS and Chip said he would add a global function for it.
I don't know if it slipped through the cracks and was forgotten or what, but I would love to see some API to allow us to "properly" set and remove waypoints.