Krystal is more likely to appear in a general direct which includes information on the new Star Fox game. But given how early that game was in development we will likely have to wait for a random and unpredicted reveal, much like Robin was.
I agree that nothing Smash-related will be shown during the Hyrule Warriors direct.
However, I have to bring up an interview with Miyamoto regarding Star Fox Wii U. Miyamoto has been working on the new Star Fox title for about
7 years now (well, experimenting, at least). What this means though is that most Nintendo devs, including Sakurai,
should be aware of the constant work on the new Star Fox title over the years. Some people (not you) argued about the franchise's relevancy---this effectively throws that argument out of the window.
The reason why I brought this up again is that you said it was early in development---which could be true, seeing as how all these years spent, as far as we know, were on experimentation. It's possible that the demo shown at E3
wasn't the current build, as that was done with Smash Brothers (and
that was publicly playable). Only time will tell, I suppose. I thought it'd just be an interesting bit of information to bring up.
http://www.nintendolife.com/news/2014/06/e3_2014_shigeru_miyamoto_confirms_star_fox_for_wii_u
I agree, if Krystal is to be revealed, it will probably be with a general Nintendo direct.