Short of the situationally unaware, we KNOW that downloading ebooks from the darknet is illegal. Which is what the original article is talking about and I don't believe that most people of my generation are so naive as to think otherwise.
We DON'T KNOW if the thing we buy from a store is illegal or not but TRUST that it is legal enough to cover our butts and keep us (as consumers) out of legal trouble. The store may have issues though. I agree there is gray area if the store has not done due diligence. But I don't think end-consumers are held accountable (or should be) for that sort of thing.
I think I'm agreeing with you, kind of. It's kind of like the difference between buying a TV that "fell out of a truck" and buying one at an electronics store. You KNOW the first is stolen, the second you have made a good-faith attempt to buy legally. It could have been stolen somewhere along the chain but you have no real reason to think so.