They are not a big issue for me at all, I'd get rid of them. I'm just aware of the fact that it's a big issue for other people, so I was trying to find some kind of compromise; and in the process found that the original Privateer has this inconsistency. So, might as well correct the inconsistency, and blame the goofiness on the programmers that programmed the navigation computers... ;-)
EDIT: And in fact, to make it clearer that the balls are computer projections, we could have that some of the new ships, or newer radars, project balls of a different color, say green, or nothing at all except a reticle, or some might project a wire-frame polygon. The idea of projecting a sphere or solid around the jump point is to let the pilot know whether the ship is within the jump point's extent; but this could also be indicated by a dashboard light.
EDIT: And in fact, to make it clearer that the balls are computer projections, we could have that some of the new ships, or newer radars, project balls of a different color, say green, or nothing at all except a reticle, or some might project a wire-frame polygon. The idea of projecting a sphere or solid around the jump point is to let the pilot know whether the ship is within the jump point's extent; but this could also be indicated by a dashboard light.