Eco-certification is, as you say, an independent process. These are not government agencies or companies that do it. There are independent organizations at the world level—the Marine Stewardship Council is foremost among them—that establish the parameters for certification, and they are the ones that certify.
What you say about the change in the landings, or maybe the condition of the resource, is interesting. In my experience, from some of the certifications I've looked at, it's less about what the condition of the resource is but more about how well you understand it and how you react to what the condition of the resource is. That is important for certifiers to see.
They understand, as we see in the Newfoundland shelf, that resources can and do change over time for both controllable and uncontrollable reasons. They factor that into their certification. Otherwise, I think it might be unfair to penalize industries that are trying to do the right thing but the resource is simply not responding for reasons that can't be controlled.
Resource levels are important at some level, but what you do in reaction to those resource levels is much more important.