I dont' know if there is a difference between fredding for The Babylon Project ( what I do exclusively ) or normal FS2open, but...
1.
NAVpoints are mostly for used for ... appearing in player hud

The have arrival and departure clues, meaning they appear and vanish.
2.
WAYpoints or even waypoint paths are used to set destinations for computer controlled ships. They have no appearance ingame whatsoever, and are used by mission designer to let ships fly certain paths or to head for certain destinations.
3. If you want to have a nav to appear a ship can autopilot to, you have to set a navpoint AND a waypoint there. The navpoint for appearance in hud, and the waypoint for the AI. The specified ship has to have the order to follow waypoint path, with THIS special waypoint set.
Well, just my point of view, but it works for me.