Nintendo told the website that "We cannot comment on the specifics of what will be announced at E3, but at the very least there won't be anything like what Mr. Hamamura suggested, so we would like to clearly deny this." The statement continued "We're having a hard time understanding what kind of evidence [Mr. Hamamura] had for saying this."
Conspiracy theorists can read Nintendo's aggressive denial as confirmation, of course. They didn't say there wouldn't be any new hardware, just that there won't be exactly what Mr. Hamamura suggested. Which means that the new hardware, if it exists, is something other than a minor upgrade.
Would Nintendo really have such a hard time figuring out why Hamamura would predict a new hardware revision? It's been over two years since the last one, and if history is any indication, Nintendo is due to drop a new system on all the people who just bought one.