Nintendo ARE going to be at E3. They confirmed themselves that there are going to be two smaller conferences in the same place, with some Nintendo directs on the run up to E3 (likely showing the titles that are going to be AT E3)
They just aren't gonna have a huge presentation. As you see when you watch E3 there are still other companies there like rockstar, valve etc who don't have a conference yet still get coverage.
To be fair how many of the previous E3 shows were a waste of time? Last year Nintendo spoke all about the Wii U while doing no specs or price, Microsoft spent half of theirs explaining how you can link yours with a phone/TV/fridge while Sony spent a quarter of theirs trying to sell a Harry Potter book. And then we see the likes of Ubisoft and EA dragged onto the stage (despite having their very own conferences) to show how Rayman/Battlefield/Fifa looks this time.