this is a potential city killer, which Kei has said would move the EN to a bad equilibrium w/r/t "the continued existence of the human race"
A dozen Jonin are also a city killer. The difference between them and something like the EM nuke is the nuke is sudden, a single technique (or seal/rune) cast with no prior warning or means of defense.
The air dome vacuum idea, however, has multiple points of failure. You can see it coming, you can defend against it. Yes, it's a very large area trap, but once people are aware of its existence they can develop countermeasures.
The EM nuke can be set off from high enough in the sky that guarding the air space is effectively impossible. The Air dome has to be set up... Maybe not right in your face, but close enough that with vigilance and given the length of time it takes to infuse a rune, you could catch the saboteur.
The EM nuke is effectively a force of nature. You can't block it, you can't stop it, undo it or reverse it. You can only run, and even then your chances are slim. But with the air dome vacuum, you can develop countermeasures. You can try to disable the dome itself, you can pump air into it to replace the air being removed, you can set up your own air dome and create a pocket of atmosphere, or do the same by tunneling into the ground.
The biggest advantage of the air dome vacuum right now is that nobody's ever seen it before. They don't know to expect it, they'll have no countermeasures prepared. The first time we'll use it to great effect. Any time after that, the effect diminishes, until it could hypothetically become another regular facet of Ninja trap warfare. "Welcome to infiltration 101, where we'll reach you to avoid triggering the explosives, watch for the force wall waiting to bisect you, and learn how to spot the signs of an air dome activating so you can counter it in time."
It's a city killer in the sense that it's potentially dangerous enough to kill Akatsuki and large enough to catch them even if they try to avoid it. Any and every essie-killing weapon must meet those criteria by necessity. I'm pretty sure the runic explosive could take out most of a city too. The cities in the elemental nations are relatively small.
But it's not an existential threat to life in the elemental nations as we know it. Once you know it exists, you can counter it.
If you really want to be safe about it, design it in such a way that it can be easily countered, (if you know how, which Akatsuki won't.) Develop that countermeasure before ever deploying the weapon itself. Hell if you want to go overboard, let the countermeasure be 'stolen' and spread to our enemies so there's no call to ever use this particular weapon again
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