What do the icons on the Historia Crux represent?

They correspond to the number of gates in the area:

  • White gates are still locked, requiring an artefact you haven't found yet, or an artefact you've found but haven't brought to the gate yet.
  • Orange gates are unlocked and usable.

Because you need to unlock gates as part of the main storyline, you'll undoubtedly have orange gate icons for most of the locations by default. The other ones unlock optional paths and are usually unlocked with wild artefacts found in optional parts of the area.