Nintendo as a whole? Yes, they will be relevant and I see no reason for why they wouldn't be. Wii U is a failure but as long as Nintendo supports it with good content it should be able to finish with enough momentum to avoid irrelevancy in the home console department. That's assuming Nintendo doesn't handle the transition as badly as they did last time. But that's just the Wii U, Nintendo also have their portable console business and their Mario, Zelda and Pokémon, and they've just taken their first step into the mobile place.
Nintendo will be irrelevant when they no longer can sell any hardware or software and the thought of having their games on mobile platforms, PC, Playstation or Xbox is met with indifference from both consumers and the industry.