My personal recommendation is that if an expensive car appears in Used Cars or Legendary Cars, and it comes in multiple colors, I'd make sure it's in a color that you personally prefer. Otherwise, if it's something like a race car, or something that only has a single color/livery, I can see myself waiting until the next time it appears. I know we can re-paint cars, but some cars have neat factory decals that vanish if you paint the car another color. And even if they don't have those, I really prefer leaving some of my cars entirely stock, including the color.
I'd have this apply even to cars under a million credits, like the Toyota 2000GT that recently appeared in Pegasus White.
Otherwise, if you plan to tune and customize the car in question, I'd say the color doesn't matter. That's what I did with a Nissan Skyline GT-R (KPGC10) that I bought from Legendary Cars, as it was white and not silver like I'd prefer it to be. In fact, I specifically re-painted it in Millennium Jade after installing a widebody on it.