While that makes sense in IRL principle (though even I myself don't know the full adverse effects of EMP on organics), it's important to keep in mind that the novelization has the EMP having a negative effect on Godzilla's atomic ray, so in my mind, it's at least possible for an organic entity to be affected. However, a tiny bioelectric spark for the beam vs. being an electricity eater are vastly different on the spectrum. A simple EMP or a consistent "weak" sphere of influence I don't think would be enough to shut down Neronga's electric capabilities (at most, just make him feel weird if he isn't invisible).
(Shin Ultraman spoilers) Even if the EMP did hit him on the nasal horn, the energy output I feel needs to be intense to blow him up; Ultraman's Specium Beam has a ton of power behind it. But anything the MUTOs throw at him would probably be naturally absorbed (like the lightning he's able to draw at the beginning), so I can envision Neronga's horn pulling in the surrounding electricity through his nasal horn or his mouth.