Perception is reality, people perceive the 240z as the original and better car, somewhat lighter, less emissions constrained, better performance etc.. Hence people value them higher. The RS30 as you say is the same car just different dashboard, rear lights, other trim items etc..
I think the North American market has a lot to do with it, they don't rate the 260z's much. Most talk about the 240z or 280z's but the 260z is often forgotten. So they are better value for money in that respect.
I could go on a long list as to why I prefer the early S30z's over the later ones but that is personal bias.