from the NYT article [1]: "The achievement was particularly impressive because the team decided to enter the contest at the last minute and designed its software with no specific knowledge about how the molecules bind to their targets. The students were also working with a relatively small set of data; neural nets typically perform well only with very large ones."
NNs in general have enjoyed lots of successful practical (commercial) applications in pattern recognition though they were sort of replaced in the "state-of-the-art" by SVMs in many cases until RBMs and DBNs came along. I agree with your caution for skepticism though, only time will tell how good DBNs are.
I think the black box criticism is BS for the most part. In some cases (google's search being a famous example) it might be great to have a human readable and tweakable solution (assuming you have the resources) but for something like recognising handwritten digits from images, not so much.
[1] http://www.nytimes.com/2012/11/24/science/scientists-see-adv...