As it has been said over and over again:
The orieentation of the HDD is not so important as secure mounting.

The debate over horizontal vs vertical mounting will rage on until solid state drives become cheap enough for the average joe hobbyist to purchase.

ANYTHING is prone to damage from vibration. It all depends on the intensity of the vibration.
With a motherboard, lots of vibrations can cause components to come loose and render the board unusable.
It's not likely that the vibrations in a vehicle would be strong or intense enough to cause damage to a motherboard. The more likely scenario is a heatsing/fan coming loose causing an overheating issue.