As Annonymoose and I discussed in a past thread which I'm still trying to find a link for, it seems the reason Hydaelyn has 'gone silent' is that She probably feels that we can basically be left now to manage on our own without Her having to hold our hand every few steps, as the 2.0 story was pretty much the
Mothercrystal carefully preparing us to become a Warrior of Light, to face down the Ascians who were the real power behind Gaius's throne and thus foil their plan to rebirth Zodiark - giving us the tools and the knowledge to do so (ala, the Echo).
With Gaius defeated, Lahabrea's hold on Thancred broken and the Garlean advance into Eorzea effectively ended, if not for good, we've attained the necessary level of power needed, and thus she gives her 'goodbye and goodluck' speech in the ending, leaving the future of Eorzea solely in our hands.
She's still there, but like a mother whose children have grown up and left home, She trusts in us to make the right decisions on Her behalf, without Her taking any active role in our Path.
As for the vision of the
'dark Mothercrystal' seen in the ending, the 2.3 story pretty much shows that Crystal is not Zodiark. Zodiark is shown to be an actual physical god, vaguely in the same shape as his FFXII namesake, in stasis and not a crystal, so what exactly that 'evil Hydaelyn' vision was of is anyone's guess. Considering the Echo cannot actually view the future but only past events from a person's memories, suggests that it might have been a glimpse of things before the First Umbral Era. Which then raises the question, 'whose memories did that come from then'?
Damnit, where's my darksteel foil hat again?