I personally prefer the trails, both in combat and sector space, but that's mostly because I have astrometrics disabled and like the sense of movement. That being said... I've discovered that with my configuration, the trails flicker out after combat and I can't get them back; only full impulse produces trails from the impulse vents. I'm guessing it's a meshing issue. I can understand not wanting them, though. Just gives me the mid-90s game feel, like Armada and Armada II. Okay, but 2D feeling.
I found recently that the "medium" setting on visual FX also seems to disable most of the engine trails, notably impulse trails not granted by engine items. "High" seems to be the only setting that includes them.
Oddly, switching these settings required restarting the game to see a change to engine trails last time I tried it, which is why it took me so long to figure out which setting did it.