If you're trying to get aspect lock on something, or even just trying to keep your bearings, this missile is evil incarnate. The EMP scrambling effect causes your target to change randomly, and the missile includes a small shockwave effect to knock you around and make sure you're not quite certain what direction you're pointed in.
The main problem with this weapon is that it's a double-edged sword, if you're too close to your enemy, your sensors get screwed up, too. The solution: use this weapon at its maximum effective range.
Even after it seemed like everything was fine, I still got some residual effects every now and then. Not the HUD flickering, but I did get some random target changes.
The EMP effect prevents AI fighters and bombers from acquiring aspect lock. This is remarkably useful in an anti-bomber role, since as long as the effect is in place, the bombers can't fire their warheads. The EMP effect will also cause AI fighters to select random targets to attack, which can either make a mission much easier (by sending said fighters dozens of kilometers away on a wild goose chase) or much more difficult (by allowing them to attack ships that would otherwise never be targeted for attack). Finally, warship turrets caught in an EMP blast will briefly cease fire.
The EMP Adv. is useful in escort missions with few present fighters, and many bombers. Be wary, however, and only mount the missile on your own fighter as your wingmen will quickly remove any hope of targeting anything for the duration of the mission.
A note to FREDders: Arming enemy ships with this thing is sadistic and immoral.
When fighting Sobek corvettes or something else with hellish AAA beams, I always pack some of these. The EMP effect gives me time to knock out the turrets before they come back online. A good strategy is to pack Tempests with these EMP missiles, just in case you accidentally get EMP splashed. On missions with a lot of bomber waves, you can simply wait at their respawn point, then EMP splash them as they jump in. Mop up quickly and repeat.
Funnily enough, the two EMP missiles inflict normal damage on "big damage" targets. Knock down a warship to 1% hull, and keep pounding it with EMPs until it goes down. It takes time and a lot of score penalty for reload, but it works.