You're ignoring a few things.
First, you don't hit the target with the EMP device. You detonate the device overhead and let the EMP hit the target. It doesn't require nearly as much accuracy as landing a shell on the ship does. It's the difference between firing a bullet at someone and landing a grenade in their general vicinity.
Second, you're assuming it's only used against a single ship. In reality, an EMP device would be best used against groups of ships. Being able to take out an entire carrier group in one shot would massively shift the balance of a naval battle.
Third, the goal of winning a battle is to win the battle, not rack up the highest kill count. Disabling your opponents ships takes them out of the battle just as effectively as singing them. Disabling may even be preferable since your opponent is likely to spend resources rescuing the people on the ships, leaving them with less to use in their defenses against your attacks.
Fourth, if you are out for kill count, it's much easier to kill a bunch of disabled ships than a group that's actively firing back and making evasive course adjustments and trying to kill you in return.
HOWEVER... most ships are already hardened against EMP (at least in the US fleet). I have no idea just how effective the hardening is (and I doubt the military is ever going to release details on that), but the whole idea of using an EMP device may be a moot point.