One is a matter of nature -- whether they are present in various bodies of water, and the other is a religious matter -- whether they render the water unkosher. The first issue I answered above. It is a simple observable fact. The second issue is a religious dispute, with the majority of Chareidi authorities ruling it unkosher, and others saying the water is kosher.
You are conflating the two issues by insisting that since the majority of those authorities render it unkosher, the first observable fact can't be accepted. I don't follow your logic on that.
As far as the historical nature of the water, all we know for a fact is they exist in the bodies of water today. Perhaps we can speculate they arrived at a later time than the Tannaim, etc. But whether that is the case or not, I don't see how it effects the first two facts.