Nintendo is clearly in a bad situation, either by their own doing or by outside sources. I'm sure they'd love to do a blowout at E3 (actually, they probably would have loved to do one BEFORE E3 with more being shown off AT E3 like sony/MS), but they've chosen not to for one reason or another. E3 is definitely not irrelevant, but fortunately, there are WAY WAY WAY more avenues to deliver a message to the press and to your fans than E3 nowadays, thanks to youtube, twitch, twitter, etc. Missing E3 is a big deal, but it's not even close to the end of the world.
Mainly, it makes E3 less fun for the fans. I don't think it'll translate to sales as much as some people would hope/expect.