I'm playing in hard mode - so I don't know if that affects anything, but I've noticed that none of the special 'prime' or 'superb' guns are appearing in my game.

The chests where they are supposed to appear are either empty or simply not there.

Are you talking about the original Call of Juarez, or Bound in Blood?

In the original COJ on PC there were no "prime" or "superb" weapons, those were only in the XBOX 360 release. Bound in Blood however should have "prime" and "superb" weapons in all release versions, afaik.