To be honest, it is sort of vague. They mention the stuff in Ultima Thule are recreations made from Dynamis, much in the way Amaurot was created, and nothing was actually alive there. We do know that the souls of the dead civilizations were basically collected and stored in Ultima Thule so they couldn't be reborn, which are presumably released after we win. After you beat the final boss, most the entities in the zone have a more positive outlook vs. the nihilism they had before. Presumably because of the "song of hope" changing things.
That being said, the Ea and Omicrons specifically seem to have the most mystery surrounding how their civilizations met their end. With the Omicrons, we get the info that they were going to just stay on standby until their power ran out because they had no further purpose. The EA were looking to get vessels of flesh, so if they died out, that means they either succeeded, or they said "fuck it" and went with the aether exsanguinators (which the traditionalists were against and seems less likely), or just lost cohesion in their crystal "houses" while staying dormant.
While the Omicron dungeon intro mentions launching nukes and shit at the planet, it's questionable if there was ever actually a threat (unless dynamis created nukes is a thing). As far as we know, they are just phantoms that think they are alive, like when the EA want to feed you Aether and get confused on why it isn't working (they don't understand there is no aether there, because they don't know they're dead). I'm thinking it was a hollow threat, or at the very least, just a dynamis created threat.
That being said, at the end Graha spends a couple minutes musing on maybe there are still Omicrons out there waiting for orders and hoping to help them. That seemed rather intentional, so I suspect the real Omicrons will show up at some point again. My bet is they factor into any future expansion involving Mercydia, the continent of the dragons. This xpac spent a lot of energy rehashing some of the lore we learned about in the Omega raids, which currently are optional and not MSQ required. The dragons have mostly been resolved from a "peace with humans" angle at this point, so having Omicrons show back up makes for a good antagonist (in theory, I'm sure there will be some good Omicrons or at the very least, Omicrons who want to stop murdering everything in the galaxy that they perceive as a potential threat or resource farm, which gets back to the themes explored in the MSQ)