According to the Department of Agriculture the hop yield for 2006 was down for the first time in ten years, yielding approximately 26% less than the year before. This might seem like a bad sign but I would not worry too soon. The variety that has been the hardest to get for my brewpub has been Hallertau, primarily Yakima.
With the incredible advance of farming technology it seems to me that the future long term is bright. New hybrids with high alpha and cohumulone yields that are drought/wilt resistant have come to the market recently, also according to what I have read the hop farmers are slowly improving their yield per acre.
The only issue that I surmise is that brewers will have to learn to be flexible with newer product coming to market. The next few years will be a great time for experimentation for both commercial and homebrewers. It would make sense that with higher alpha acids in hops that brewers will have less particles in their kettles after whirlpooling and thus increase their yields. We might even see some American varieties implemented extensively in the foreign market, which could help some of our smaller farmers although with the large commercial growers there is always a political element that could throw a stick in the wheel. I have no information to date regarding tariffs that could affect this scenario.
In the long run the issue will not be hops but barley. The current legislation that is driving the market is pushing farmers to grow corn for ethanol. It is hard to criticize a farmer for growing a crop that makes more money, even if that money is a subsidy that is coming directly out of our pockets. I anticipate that grain prices will skyrocket over the next two decades unless the political situation changes or there is another incredible advance in technology. To me the solution will lie in the free market. As long as there is a demand for beer and that demand is high enough nothing will stop the machine. Unfortunately I don't see demand increasing overall considering the rapidly aging population and challenging dietary demands. We will probably see a long term increase in the cost of beer.