In the comics, the Mk VIII armor (post-Armor Wars) used something that was called an EMP. It was a weapon of last resort because it knocked out everything in range, including the armor itself. That suggests the Iron Man suit wasn't shielded, but I don't think that weapon behaved like a real EMP either. As I recall, it simply suppressed the functions of electrical systems for a period of time rather than destroying them. Still, it was so effective against tech-based villains that Tony started making it his "go-to" weapon despite its disadvantages. That ceased after he went up against the Mandarin and found out the hard way that it didn't affect the ten super-duper-high-tech Makluan rings. ("The hard way" means he had to face a fully-powered Mandarin with a nonfunctional suit of armor. Oops.) I don't think the weapon was used again after that. I could be remembering some of it incorrectly, though.