There are no natural breath weapons. Yes poison and acid (which you didn't mention) could plausibly be "natural," but there is no "natural" creature the exhales acid or poison gas like dragons. There are things that are similar though (spiting cobra, horned toads, bombadier beetles, ants, etc.). Of course I don't what that has to do with your argument (giants have similar issues).
Dragon breath is natural within the nature of the DnD universe. Or at least, after a careful parsing of the entry on dragons and breath weapons, I conclude breath weapons are not magical, and if not magical, what then?