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.
If the evidence was obtained using illegal methods, all that evidence can't be presented at trial and the jurors can't take that information into account when deciding guilty or not. There are many people who are acquitted for things they obviously did, but for which there is no formal legal way of proving it.
This is decided in pretrial hearings. There have been entire cases based on the admissibility of evidence. If the judge rules it is or is not admissible, there is some manner of recourse or escalation for the usurped party.
IANAL YMMV BBQ
Except that if they obtained the IP illegally, and the defense can prove it, all the evidence obtained based on that is thrown out. Which is why they're pursuing it so vigorously: as you've noted, it's the code they found on the box and the bitcoins they found by finding the box's owner that pin him so severely.
Wouldn't the only evidence obtained through that hack be the actual IP and related data?
I mean, the actual box was presumably seized after a proper warrant for searching a specific physical location. The question is would the fact that his stuff was searched be considered "fruit of the poisoned tree" since the servers were identified through that IP or as "inevitable discovery" since if he's a suspect, it's standard procedure to search his stuff anyways. But IANAL so I'm not sure how it works in USA.
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.