What a difference a better guidance system makes. With a very slightly smarter guidance system, the Javelin-like is able to hit oncoming free trader: 

In this case, the ship is cruising at 150 meters, and gently accelerating (throttle at 1/3 but started at 80 m/s). The Javelin is launched and rather than just aiming for where the ship is now, it estimates flight time and aims where it will be. 

In a slightly different set-up, the pilot of the ship realizes after 1.5 seconds that he has been fired on and jams the throttles to full, and the Javelin misses by 8.6 meters: 

In part because at this point the motor of the Javelin is nearly burnt out and it does not attempt to compute acceleration of its target, only position and velocity. 

So, travellers advisory for low altitude flight over hostile TL6 worlds: they can actually hit you. Limit low level flight, and when traveling between cities on said TL6 worlds use the more normal low-speed cruise: 30,000 meters altitude at 6100 meters/second (Mach 20). Throttle set to 1/5th thrust should do it.