Actually this has already been discussed at length in the Lore forum so it would be a repeat thread. XD
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Isn't her Crystal Eye mentioned by one of the brooms in passing during those quests?
"The light from your eyes" part, I took to mean her eye color. Before, she had bright green mako eyes, now her eyes are boring.
She flat out stated after she woke up that being in the Aether so long "blinded her" and that she can only see using Aether currents now.
And then later on, Matoya mentions that if she continues to use the Aether to "see", that it will slowly drain her life force. And "losing the light of your eyes" is a literary phrase meaning "to go blind".
As to the OP, yeah, I think they'll come up with something. I don't think they're going to kill off Y'shtola with something as lame as a slow aether-sucking death. It's just a trope to cause some suspense and tension.