EMP weapons cripple an enemy ship if there is no shield, and they don't have some kind of emp resistance. The problem is that, similar to beam weapons vs shields, they are generally all or nothing. Either they hit hull and cripple the ship, or they hit shield and are worthless, no middle ground.
When they work, they are honestly far more devastating than any other type of weapon. Worse than overloading a shield, since you still have engines. EMP causes this game's equivilent of a stunlock. If they don't have an omni-shield, then they can't restore the shield to protect themselves, and a a ship disabled like that tends to die rather quickly.
Similar to my opinions on beam weapons, I really think Ion weapons need to have more generalized effects, rather than entirely negated vs devastating. The Ion beam weapons that partly bypass shields really seem like a good direction. The other one being ion weapons also doing damage vs shields.
Having all ion weapons have that kind of shield penetration (dependant on shield hard flux, I think, and having reduced effect) and being mitigated somewhat by armor might make them useful in more cases.