I don't think this is going to be a big deal-breaker for Nintendo.
The people who pay attention to the gaming side of E3, are gamers, not the general public, as a general rule.[Ha! I made a not-so-funny!]
Most gamers are going to be watching the internet for news on the show before, during, and even after the show is over, as well as watching it on TV.
Anyone who knows the name Nintendo, and has even the slightest of passing interests in what they've got up their sleeves, is going to hear about Nintendo just by being on the internet around gaming sites.[unless said sites are dedicated to other systems and don't allow talk of Nintendo, or are a hater site black-listing any positive info from Nintendo]
Nintendo isn't going to lose any coverage from the gamers that matter here, because most of the gamers on earth have some way, some how, of finding internet access to check the latest news from any of the big three.
Plus, by using Directs, they've got the opportunity to put out info on their games before E3, which is going to focus mostly on the new SYSTEMS that are coming out, which Nintendo does not have to show, since they've already done so.
By not bothering with revealing everything at E3, they're avoiding having anything they've got being overshadowed by the announcements of hardware, which generally overshadows game announcements no matter who's doing it.
Shifting the deliverance methods of their games is a smart move in this case, and I can guarantee you that they'll be back at a future E3 the very next time they have a new piece of hardware, or something super-significant to say about the tech aspects of current hardware, to talk about.