Idk, most navigation would be along or close to the ecliptic plane of the system, wouldn’t it
If you are going to and from points within a solar system, probably but not necessarily. Every transfer made between gravitational influences increases the chance that you will enter at an angle to the equatorial plane, especially if the two influences are not coplanar traveling between solar systems would likely have you entering at a significant angle. Furthermore, approaching a ship at a low velocity means slowing down as you approach them, so even if you do approach coplanar, it would be engines first and not nose first (unless star trek vessels have an ability to reverse their propulsors? I don’t know if that’s ever been shown aside from by approaching things nose first). The expanse showed this aspect of space interaction well with the flip and burn maneuvers
between solar systems
FYI, there is only one solar system in the universe.
Source:
There are many planetary systems like ours in the universe, with planets orbiting a host star. Our planetary system is called “the solar system” because we use the word “solar” to describe things related to our star, after the Latin word for Sun, “solis.” — NASA
Any ship traveling towards another ship would have its nose pointed towards it.
If both ships travel towards each other, their noses would be aligned, but their roll would likely be different.
That’s a bit different from what’s being shown in the comic where ships seem to have any orientation, no matter the context.
As for a galactic up/down, the galactic disc would be the obvious reference. That still leaves a 50/50 chance that two civilizations would choose the same direction as up.
Realistically (i.e., not in Star Trek), a ship traveling toward something will have its engine cone pointed towards it as it decelerates for rendezvous.