Why are some "updated app" dots brighter?
I noticed some of the dots on mine were a lighter color several hours after an update was downloaded, which would blow my theory about timing, so I tested changing wallpapers to see how that affected the color. This showed that the color of the dot is impacted by the wallpaper. It may be semi-transparent or the color may simply be chosen by the system based on the color behind it.

The below images were taken within a minute of each other after changing the wallpaper. The first two show changing from a light wallpaper to a dark one. The second, third, and fourth images were all taken with the same wallpaper. You can see the color darkens as the background darkens. In the fourth image, it even varies slightly between rows based on the differing shades in the background.