I'm going by memory on this answer because I can't recall at this moment the Apple Support doc that covered this (I'll have to look it up later or someone can update my answer if they have the link).
Both colors indicate that an update was performed and you haven't opened the app since that update.
The dark blue dot means the app was updated manually. This means you saw an update was available and you tapped the button to perform the update.
The light blue dot means the app was updated automatically. This means you have automatic updates turned on and the App Store checked, saw an available update, and updated the app without your initiating the update.
I hope that makes sense and that it's not vica-versa.