Actually, space in general is mostly 2 dimensional, in that all the interesting stuff generally takes place on some sort of almost flat plane. A star system is generally on a plane, so is the galactic system, and for most planet+moons too. They just tend to be different planes so for ease of communication you will probably just align your idea of down with whatever the most convenient plane is. This of course is ignoring what gravity down is, as that changes as thrust does.

And as for ship alignment, yeah no one is going to worry about that till its time to dock, at which point the lighter vessel will likely change their orientation since its easier and takes less energy. Spaceships are not going to be within human sight range of each other most of the time, even being in relatively the same are. Space too big and getting ships close to each other is dangerous!

But in media that fucks with people's idea of meeting and seeing each other so for convenience of not confusing the audience you don't see that level of realism often.