So long as you don't fiddle with the displaying settings when you make a waypoint (IE: leave them default), the WP's shouldn't be displayed ingame. However, there -is- (as always) exceptions - when you're in vehicles, waypoints -always- show up, regardless of difficulty level. Annoying, yes, but if you like you could likely do the following trics:
(I'm assuming your player is not in a group, otherwise you wouldn't see the waypoints anyway)
Create a waypoint on top of the player character, make this the first (position 0) waypoint and make it a MOVE waypoint.
Create a trigger, with 0 x/y and condition none, present. Call it "detectcadetmode" and give it the syntax:
Condition: cadetmode (might have to be cadetmode true, i'm going to fiddle with it in a second)
On activation: Waypoints=true
Create another trigger, with 0 x/y and condition none, present again, call it "CadetWaypoints", set it's type to "switch" and it's condition to "waypoints". Now, select syncronise from the menu bar (f5 is the shortcut, I think) and drag from the CadetWaypoints trigger to the first waypoint (the one directly on top of the player).
How this -should- work is as follows:
In veteran mode, the instant you start the game you will have reached waypoint 1. However, since the condition to go to waypoint 2 (it has to be in cadetmode) cannot be reached, the waypoints will simply stop. In cadet mode, the condition is naturally true and the waypoints will function as usual. Of course, I need to test this first. Mockup here we go. be back in a minute or two, I'm gunna try to get it goin'.