IIRC, the formulas state that for throwing, the speed of the thrower doesn't matter, only the speed of the target.
So riding full speed at a stopped opponent and hitting him with a throwing axe is no different than just standing there and throwing it at him -- your speed doesn't count.
If you're riding behind a horse, chasing him, and throwing at his back, you'd be doing almost no damage because you're just hitting a target that's moving really fast away from you. You'll have to save your throws for oncoming enemies.