I think I've figured out why ships "overshoot."
Acceleration, as we all know, is not only "increasing velocity" but actually "change in velocity." If you set a super-long distance route to try and exploit the acceleration (like we have all been experimenting with), your ship will not be able to decelerate to "hit" the planet. Thus, you will overshoot the planet. This could happen, I guess, any time you change course at all. I think you'd still fight any ships in your path, but probably not be able to land on a planet.
