The point is one can suppose the tendency of ships to line up is a matter of traffic customs, widespread practices to make sure that one ship does not unintentionally ram the other. Given that the majority of ship encounters at least begin with non-hostile intentions that seems reasonable; at least, it's no less reasonable than the widespread agreement on what are hailing frequencies and how to transmit visual signals.
The comments abouts planetary orbits, solar systems, and even the galaxy having preferable directions are to answer the people who insist there can't possibly ever be any non-arbitrary directions in space so how do you tell up from down. There are non-arbitrary directions, obvious to any people able to seriously contemplate travelling in space. There's local north and south and even a Galactic North and South.
(Finally I'd like to note that the Original Trek, when it did have multiple ships in the same shot, didn't bother making them line up with any particular rigor, probably because they were straining the effects processing just to have two ships in the same shot at all.)
