We still use term "dark side of the moon, even-though the far side has been photographed and mapped. Some terms just stick.
What’s the alternative? The side of the moon we can’t see? The ‘Other’ side of the moon?
The dark side of the moon is still called the dark side of the moon because the name remains descriptive and apt.
You might be right, it could stick, but we don’t know what dark matter/energy is, we can only observe the effects. When we know how it works, we’ll have a description of its properties and probably a bunch of new names for fields and particles.
Another reason to avoid dark matter and energy is that the scales they operate on would have as little narrative impact on the characters as it would in any other show.
I suppose, maybe, a precisely calibrated operation like a transporter could be a affected by a one in a trillion WIMP collision with a baryonic atom.
A time travel equation might be affected by dark energy with comical results. Maybe not.
The one dark thing that did capture my imagination was the Dark Flow, but last I’d heard was that it didn’t exist.
What I would like to see tackled in Trek is the Holographic principle, that one I just can’t get my head around.