I don't know if Nintendo wholly own the Eternal Darkness IP. They have a patent on 'sanity effects', but from everything Dyack's said the actual Eternal Darkness IP is a bit more complicated. Chalk up the fact that Nintendo still has shares in Silicon Knights and yeah, it's a bit of a weird situation.
I'm sorry, this is a few pages back, but no, it's not "complicated" at all. Dyack and SK don't own the IP in any sense of the term. Nintendo owns the gameplay mechanic, they own the trademarks to the name "Eternal Darkness". The only thing that's complicated about it is that Nintendo still has a partial stake in the company, even though SK hasn't made games with them (this has been confirmed by Dyack in interviews where he calls Nintendo their "silent partner"). That would make it complicated in the way that Nintendo might not want to piss off a developer it still owns a stake in. But if push came to shove, Nintendo owns all the components to do it.