why are monsters invading the cities?

[Alaltus]

It's all still Canon, Atomos is summoning all these creatures through time/space.

Just because he is dead in our world, doesn't mean he is dead in others. Atomos simply goes to a time he was still alive and copy and pastes him back to life. It explains all the monsters and Naels that attack the city.

Its just as possible Atomos has nothing to do with any of this and is simply interested in harvesting the aetherytes for his own reasons(or whatever it is that he is doing to them), the voidsent creeping through the cracks that process creates. After all theres nothing really giving him a motive to create Nael van darnus' to attack Uldah since he's been going about his business pretty much unfased this entire time he didnt set out to attack adventurer's only ones that are a threat to his continued feasting(or whatever).

Far more likely the entity causing the current attacks is related to Dalamud itself since not only voidscent and Nael van darnus' are attacking but also monsters of all kinds when by all accounts they should be fleeing. Either monsters are being possessed by some sinister evil or they are being attracted to Dalamud which Uldah happens to be in the path of. As was said earlier Nael's essence was seen entering Dalamud so its not so far fetched that Dalamud is related to the sudden appearance of Nael clones.