The SCH quest tells us that the Nymians never realised it was a Mhachi ruse, at least as far as the Tonberries know. The believed it was some form of magical disease from the southern Isles. They didn't put together the truth till the SCH quests. The always believed the original source of the plague was the sailors, not the stuff they brought back. This only works because the Voidsent in question is almost completely undetectable. The Nymians never knew it was there.
The main reason I brought this up again is that I discovered in finishing the SCH relic, The Last Resort, that the original Zodiak weapon belonged to a Nymian SCH called Golbas Rombas who was credited with saving the Nymian people from the 6th Umbral Calamity. Combined with the fact that the Sightseeing log at the site of the Floating City of Nym says modern scholars believed that the City was destroyed in some type of disaster involving Aetheric Wind, I speculated that Golbas Rombas might have tried saving the Nymians by literally levitating the city. After all the relic is called the Last Resort.
On the topic of the Allag and the Elementals, there is obviously several possible options for why the Allag didn't suffer the same fate. Its possible they found a way to supress or pacify the Elementals. I personally suspect, being a group that far surpassed any civilisation since in their understanding of the nature of Aether, they recognised the nature of the elementals as nature spirits and they understood the importance of Aether in the natural world to produce a healthy environment.
The other thing you have to consider is that the Allag didn't power their magics the same ways. The Allag produced magics that civilisations of the 5th astral era almost certainly didn't manage to replicate. However the Allag tended to power their magic from concentrated power sources like the Crystal Tower and Primals. The Elementals aren't concerned on morality as much as Balance and the natural order. As long as the Allag weren't screwing up nature, the Elementals were probably pretty tolerant. They also seemed to be more tolerant back then in general.
The War of the Magi introduced a form of Magic that drained Aether from the world around the caster to power his or her spells, allowing much more powerful spells than a individual could cast without the aid of a power source like the Allag used. The War, and the arms race that was born from it, resulted in an ever escalating drain on the Aether of the natural world. They were literally sucking the life out of the land. This was too much for the elementals which is why they unleashed the flood.