Re: Flares from Iron Man
This is true, but at the velocities normally associated with flying, the target usually isn't in the vicinity if the counter-measures work as intended.
Re: susceptability complications and autofire
Damage from a Susceptibility is STUN.
An EMP blaster would be a specialized weapon, but it is still an attack. Susceptibility is normally things that don't affect the majority (Superman and kryptonite).
What you would be looking at is a Vulnerability towards EMP attacks.