This actually puts Nintendo in a pretty good position. There aren't any big name Vita games I can think of coming out this holiday season, so the Vita isn't going to be a big seller. However Nintendo has some big name games coming out for both 3DS and Wii U, and with no handheld/home console to compete with, they stand a good chance to make up some ground with the Wii U, and extend their lead with the 3DS.
Nintendo is probably thanking their lucky stars at this point.