That said, it's hard to argue with Clay Risen's observation that, "If a [bourbon] bust comes, it will hit the craft sector hardest." But then, the bourbon boom is a very different experience for the big distilleries than for the small ones.
Speaking for myself, a key way the bourbon boom helps craft distillers is that it accustoms bourbon buyers (by which I mean me) to prices in the $40-$80 range. Craft distillers need buyers to pay $40 until the distillers are able to make bourbon that, tasted blind, is worth $40. (Adjust the prices to your local market.) So, while the boom allows the major distilleries to make a nice profit, it's pretty much essential to the craft distilleries for their continued existence.
I think we can also distinguish between a boom -- now measurable in billions of dollars -- and a fashion, the latter a matter of barrel-aged locophilic cocktails and the like. When something is in fashion, the quality is a secondary consideration, but sooner or later the fashions change.
In a few years, we will have a lot of small distilleries with enough stock and experience to be making high quality whiskey. Not all of them will, though, and the ones that haven't figured out how to do it will
Or -- to put it in happier terms -- maybe craft distilleries will follow craft beer, not so much with an extinction cycle as by becoming unremarkably common. Maybe they survive the fashion of overpaying for underaged whiskey, get their value and cost better aligned, and settle in as respectable local or regional distilleries.
(Though of course the comparison will always be inexact, not least because the major breweries don't make very good beer, and their not very good beer won't improve with aging and blending.)