I share that concern in general (and in particular with regard to software patent cases, which often cover highly technical material and where the jury has no context about the novelty of the patented inventions), but I think this case is pretty much a slam dunk however you approach it. Regardless of how they obtained the IP, they got to the box to find it running Silk Road code, they got to the box's owner to find him holding Silk Road bitcoins, etc.
This isn't a case that hinges on a technical nuance. It will be practically impossible for DPR to convince a jury that there is any reasonable doubt as to his guilt.