Their primary naval weapon is a missile that can get into ballistic mode before a ship's countermeasure can intercept it.
I'm not sure what you're after there. A ballistic missile is one that follows a suborbital path (shitloads of power in the boost phase, and gravity and minor steering after).
Even leaving that aside, AFAIK, the only serious countermeasure that the USN has for unguided missiles is Phalanx. I would think that relatively slow, small, unguided missiles* would be meat for the Phalanx. You could probably overwhelm the system, but that assumes the USN has no way to deal with said speedboats *cough* artillery *cough*
Hell, you don't even have to hit the boats -- just throw up enough of a barrage that they don't get a stable platform long enough to take a shot.
*The kind of MLRS that fits on a single engine fiberglass boat doesn't lend itself to having large munitions.