Venat's reasoning can be summed up in two points:
1. "I don't want to cause a panic."
2. "We still need Hermes' expertise on dynamis."
Given one depressed Ancient inadvertently ended up creating what became a truly omnicidal menace, I can't see a whole society of them knowing their end is inevitably nigh especially considering they'd rather kill themselves than confront their grief ending well; and like it or not Hermes was the foremost expert on dynamis and entelechies, and said expertise would be needed to see them through the Final Days crisis (implicitly, to help fashion Zodiark).
No, I don't believe turtling behind Zodiark forever was a proper solution. Even if his aetheric barrier lasted indefinitely, the Ancients would more than likely have gone the way of the Plenty once they reached their "perfect paradise... free from sorrow," given they were already doing that on an individual level.
That's not totally accurate, but it does bring up another plot hole I've never seen anyone else point out. (Guess those only matter when you disagree with a character's reasoning.)
The dip in aetheric levels across the planet was due to the influx of Light / Umbral aspected aether from the First slowing the world's aetherial circulation. Shadowbringers reveals to us this is due to the Rejoining process, whereby a reflection's aether seeps into the Source, causing an aetheric imbalance, after which a Calamity is triggered on the Source to complete the process. (Apropos of which, wasn't the lower aether levels hinted at in 2.5, which got lost in the drama of Wilred's murder, the Braves' treachery, and the disastrous banquet? I didn't forget, it just wasn't addressed.)
The problem is Y'shtola sees this as evidence that a Calamity is nigh due to the same thing happening before Dalamud's fall... but that Calamity was Dark / Astral aspected, so aether levels should have risen across the planet.