Yeah, it's all a BS reason to can a project. I'm not sure why anyone in that universe thought it sounded remotely valid. Maybe they don't but they just run with it because no one has the physical might to say otherwise.

The EMP wave is... super effective. The internal wiring at least needs shielding. I'm not sure if they can do anything about Funnels being jammed. I'm sure it'll come back as a weakness during their next encounter with this EMP-Not-A-Gundam because it doesn't sound like anyone alive knows they got jammed.