Well, you actually encountered fighters between navpoints quite frequently... still, the point of the missions wasn't to check those particular navpoints, but to check the whole route. The navpoints were just places along the route where you were supposed to change direction.
Does FS2 have some kind of neutral alignment thingy? As in, in WCP you can make a ship Confed, Kilrathi, Alien, or neutral, with neutral ships not being shot at by anyone (except aliens, sometimes). If you have such a possibility in FS2, then you could simply make a ship with no mesh (or a mesh with transparent textures) that would be used as a navpoint of sorts. If you had that, then it would just become a matter of the mission script activating and deactivating ships in such a way to make it seem like only those in radar range of the player are being shown. The player would still have the tedium of flying between navpoints with no autopilot, but for WC1 missions this wouldn't be a problem, since the distances were so small in WC1.