The problem here at the moment is that there are only 2 options for the hudwp(the shift-click waypoints)Its either 0 or 1.
Basically when you have hudwp and hudwpperm to 0 in your server-settings you can still use them when you are in the littlebird, jets and in some more vehicles. While they should be gone for everything when server setting is 0.
Thats the problem/defect as it is now while this is also a request to add more options to the hudwp settings. For example: Pilots need the waypoints to perfectly land on LZ markers. Without the shift-click marker a pilot would be forced to look on the map while flying and therefore can't launch countermeasures when AA is comming in. And landing with a GPS also won't be as precise.
Therefore here are some suggestions on how these settings should be:
HudWp=0, Means no shift-click waypoints for anyone in any vehicle or on foot.(currently already is like that, except for stated vehicles)
HudWp=1, Means shift-click waypoints enabled for everyone.(currently is like that)
HudWp=2, Only shift-click waypoints when you are piloting a air vehicle.
HudWp=3, Only shift-click waypoints when you are driving a land vehicle.
This way you get more options on how the waypoints are managed.