Many craft breweries contract their hops out in advance. Some buy hops on the spot market, and those breweries will either have to alter their recipes or adjust. Simcoe and Amarillo in particular are funny hops, as I understand it they're patented and only grown by one grower (YCR), and have been victims of their popularity. Dogfish Head alone accounts for a fairly sizeable percentage of the simcoe harvest each year.
I was lucky and heard about this shortage a few months ago, so I'm sitting on two pounds of leaf and three pounds of pellet in my freezer. Here's hoping it lasts.