If this were a discussion of Japanese conviction rates based primarily on (coerced) confessions or something like that, then yes, a 99.6% conviction rate would be suspicious. But you have to remember two things here:
(1) 99.6% is not that much higher than the usual federal prosecution rates (I think they get a net of ~96% when I looked it up a few months for a different discussion),
(2) and when Baranoff says “We don’t build our cases on one piece of evidence. Our cases are built on evidence that is curated over many years. We take our time to build these cases to make sure we have them right.” (the part you didn't quote), he's not kidding. That's exactly what they do with cyber-crime cases. They spend years investigating an organization or figure, flipping people, running markets or forums, extracting records from ISPs and Amazon and Google, and so on and so forth. Look at the whole tangle of carding cases in the 2000s with cardingplanet/shadowcrew/etc. For that matter, look at the Ulbricht Silk Road case right now - the agencies involved spent years busting random vendors, looting people's emails (eg Ashley Barr's Gmail was searched on only the vaguest possible suspicion), flipping multiple employees... Read the trial transcripts if you have a few days to spare.
If anything, I'd say that a rate of 99.6% says bad things about them, but for an entirely different reason than you: because it implies that they're inefficiently overdoing their cases, goldplating them & gilding the lily.