Last month Nintendo let the Eternal Darkness trademark fall through, but the company took the time to finally get it re-registered on February 10th.
Whether or not Nintendo actually has plans for the franchise is unknown at the moment. The last we heard from the development team behind Eternal Darkness, Silicon Knights, is that the cards were still on the table with Nintendo and that there was a strong change the series would return. But, we haven’t heard anything regarding the franchise recently.
Or Nintendo could simply just be protecting the term.