Walt had also essentially closed the book on the ricin by "finding" it in Jesse's Roomba, so the only way he could put together that Huell had swiped it was if he also believed Walt snowed him back then, too. That does fit with the rest of this episode, and Jesse's general complaint that Walt is always "working" him. Definitely some tricky dot-connecting going on for Jesse to figure all that out, though.
Walt's confession was just brilliant. He linked pieces of the truth together with lies that would be difficult or impossible to confirm, as the relevant players are all dead. Jesse is pretty much his only weak link at this point, and as a matter of self-preservation, Walt should have pulled the trigger on him.
But it's just as well that he didn't, because I'm more than happy to see Walt's perfect little world upended by the troubled young man he's abused for the past year.