I don't think telling investors the NX won't be present at E3 is wise if the opposite is true. They might say nothing, but when money is concerned if Nintendo says it's not there, it's not there.
I'd say the entire situation is just a perfect storm for Nintendo. In the negative sense, or at least when it comes to preparation. The Wii U failure would have forced their hand to move into new technology, and transfer over software, very quickly. A lot of scrambling, so issues there alongside the typical teething every company goes through during a hardware transition. Nintendo's hand has been forced, in that respect, and I'm guessing earlier than they would have hoped. Iwata croaking would have left a huge dint too, no matter how prepared he was (and I'm guessing his preparations were incredibly thorough), as losing a very hands-on CEO during a transition can't avoid an upset in efficiency.
I feel Nintendo probably wants to make the NX reveal right. Hit the hardest they can. They can't predict how it will go down, and the Wii U would have been perceived as a far weaker impact than desired. And dumb mistakes made with the Wii U have probably (hopefully) settled in. You can't half bake the reveal, especially if it's due early next year. Thus any lull in software development and hardware stability, from new titles looking and playing their best, to transitioning in-development Wii U games to a presentable format on the NX, are going to leave a negative impression if they shown too early or absent from a scheduled reveal. Whether or not Nintendo is having issues on the hardware and software front is impossible to know (and it's entirely possible that they are having issues), but there's valid reasons with either answer for delaying the entire reveal until an exclusive event later in the year. An event where the hardware can be shown off in full, and a proper software showcase can sell the product for a release only a handful of months later.
Plus Nintendo isn't the only major distributor who doesn't really give a fuck about E3 these days. Yes, all eyes are on E3. But in a modern connected world it's hard to give a fuck in the grand scheme of things. E3 is in some ways a bit redundant, and if a company has the money, showmanship, and product, huge reveals that leave a big impact on potential customers can be done entirely at another time. Rockstar don't care. Bethesda generally don't care. Sony has done similar. Microsoft too. Yes, people will whine and moan that Nintendo gave up, lost E3, or whatever else. But all of that will be forgotten and rendered meaningless in an instant should an exclusive event later this year blow socks off. Hypothetically, an October or November event comes along, huge exclusive press event, and the NX looks fantastic with an extremely impressive showcase of software, you can guarantee it'll be all over websites, tech mags, and so on and nobody will be going "oh but they weren't at E3 remember that so the NX actually sucks and nintendo is doomed".
Worry when/if the end-of-year event gets delayed into 2017, or it's a stinker when the time comes.