Anything but Story = not story. His involvement was making Konami give it back the Castlevania name and placement, and advising on Gabriel's character design, to make him less brutish. He pretty much existed solely to give his blessing to the project and help sell it because his name was attatched. That's about it...
Oh, and voicing the Japanese chupacabra.
Yup, Kojima was only there to "oversee" the game's progress. As for his actual role, it was strictly advisory.
Voicing the chupacabra? I can't tell if that's a joke or not...
I agree with Intersection and Lelygax. The quote just affirms something we have already known for years. I don't think a Konami employee is allowed to confirm or deny who is working on a project that is still under wraps. We already know a new 3DS game is being worked on. Maybe by IGA, maybe by somebody else. We can't tell.
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I never knew about a future 3DS CV, either. But, in any case, it would seem pretty logical for Konami to continue the series on Nintendo's handheld; it's done that since the early GB days. Even though its first 3DS outing left much to be desired...
As for the rumor, I'm not sure how I could have missed it, since I'd already been perusing the forums (from the outside) by the time it was posted... these things happen, I guess. As for the rumor itself, well, these rumors often turn out to be true...