Did Zodiark ever do anything wrong?

[Dikatis]

The Ea mention two planets, both of which sound like they could be their home, but it seems strange one way or another.

I don't think the Ea experienced the Final Days. The Ea's home is designated as Ostrakon Tria in Meteion's report, and this is what she had to say about them:

Tria: Evidence of large population centers akin to cities recovered. No extant life-forms found — only their lingering essence.

One race had concluded that finite time was the root of all woes. Aspiring to shatter its shackles, they went in search of infinity. They discovered nothing is infinite, and that neither time or death can be cheated. Disillusioned, they gave up on the future — and themselves.

The Ea had already discovered the inevitable heat death of the universe and had exterminated themselves via exsanguination of their aether before Meteion got there. She presumably got information on them via an Echo-adjacent power and her own abiltiy to tap into the emotions of others.