Jump Holes have no strict size. All that you see in space is an indication of a spatial anomaly; it is actually space dust being drawn into the gravitational epicentre of one end of the Jump Hole (and leaving it, too, since two-way travel is possible).
The Jump Hole's gravitational pull drops exponentially as you move away from the epicentre, hence making them appear small.
Edit: Navigation Beacons aren't really necessary, considering that we're on the way to having functional Jump Drives (for Capital Ships and possibly very big transports).
Still not a bad idea, though, if you wanted to represent short-range Jump Drives.
