My answer is in large part an expansion on Old Brixtonian’s comment.
As he says, the first sentence contains an error (perhaps merely typographical): “how is it what” should be “how is it that.” As written, it is nonsense. But your understanding is correct that the intended meaning is
If they had really …, why are there …
The second example is a mess.
I agree that story is important but what is story.
Ignoring the missing article before the second “story,” this sentence uses the word “story” in two different meanings. As a result, it makes no sense: how can you agree that something is important if you do not know what that something is. The intended thought is
I do not agree that the plot is important to a story.
The phrase “I agree but” is a way to state partial agreement at best. Here the following sentences make it clear that the speaker does not agree at all.
The intended meaning of the third sentence is expressed very unclearly. It could be construed to mean that the number of plots that have been used by many story tellers is very small. In context of course, it is obvious that this construction is wrong. What is intended is something like:
Few if any stories have a basic plot that is original. How many stories are variations on “boy meets girl; boy loses girl; boy gets girl”?
The conclusion is not even a real conclusion but rather a meaningless question:
If it is not just what happened, is it how what happened happened?
We can sense a general thought there, but it is vague. You did well to decipher what you did out of it.
This may have been what the author had in mind.
I do not agree that the bare plot is what makes a story appealing. There are only a small number of plots to work from. It is how the story teller embellishes and elaborates the basic plot that makes a story interesting and appealing.
If that or something similar is what the writer intended, it is a cogent thought lost in a maze of careless expression.