It's a variation of the common phrase "Absence of evidence is not evidence of absence."[1] It's a common debate, at what point, if ever, can we say something doesn't exist when there's no evidence for it. There might actually be some evidence that organic food is healthier, this study[2] found an association between organic food and reduction in non-Hodgkin lymphoma.
In that exact same book by Carl Sagan he uses the quote:
> Appeal to ignorance—the claim that whatever has not been proved false must be true, and vice versa (e.g., There is no compelling evidence that UFOs are not visiting the Earth; therefore UFOs exist—and there is intelligent life elsewhere in the Universe. Or: There may be seventy kazillion other worlds, but not one is known to have the moral advancement of the Earth, so we're still central to the Universe.) This impatience with ambiguity can be criticized in the phrase: absence of evidence is not evidence of absence.
Carl Sagan says we should be comfortable with ambiguity. We should say "organic food might be healthier, or it might not, we don't know".
But I already linked one study that seemed to indicate a health benefit.
I don't see how "The Dragon in My Garage" is relevant here. In that story, the goalposts are constantly moved until the idea is untestable. But the idea of organic food being healthier doesn't seem to have moving goalposts, and it doesn't seem untestable to me.
[1] https://en.wikipedia.org/wiki/Evidence_of_absence
[2] https://www.nature.com/articles/bjc2014148