I'm level 62 and I've still not found two waypoints. I did notice for at least a couple of waypoints that they're found through side quests. Anyone have any suggestions for which side quests to do and how / where to find them? How many waypoints has everyone else found?
The easiest way to figure out which ones you are missing would be to use one of the interactive maps where you can check off the ones you already have. (I can link the map I've used, but don't want to unless you want it.) As far as I know the only waypoints that are locked by quests are the ones attached to strongholds.
Just to correct the post a bit: there's no need to do any sidequest to unlock all waypoints.
https://d4builds.gg/map/, enable waypoints from the filters, compare to your own in-game map. If you run to a missing waypoint and it shows as locked, you'll need to clear the nearby stronghold to open it. There's a total of 6 waypoints which are placed inside stronghold areas.