Because they've never had lackluster E3 conferences.
Even the confirmed games alone would be more than enough for a conference with the usual padding of shit we don't care about.
Hell, the first showings of MK, 3D Mario and Smash Bros. alone would warrant one.
Why are you assuming a dedicated press event and a dedicated consumer stream (and more things but I doubt anyone cares about the retailer event) are somehow less important than a single conference anyway?
Because thats is now how you attend E3 as a console maker, I'm sure Nintendo is doing all they can to reach their dedicated fanbase as much as possible, the direct feeds show this. But from afar it seems needlessly drastic to skip the BIG spectable. . Also Nintendo has had lackluster E3's, everyone has.