You know, they've actually developed prototype artillery shells than can adjust their trajectory in flight to compensate for any wind conditions or drag that's making them deviate from the desired course? (I remember seeing a thing about that on one of those "UNGH FUCK YEAH HIGH TECH WEAPONS AND SHIT UNGH" that were popular on discovery and the like before they started just spamming reality shows about fishermen and rednecks driving trucks for god knows what reason.) That's a guided projectile, but is certainly not what in common parlance is referred to as a "missile".
A drone that carried its own guidance software and had no link to the outside world wouldn't be very susceptible to jamming, and if launched at a significant fraction of the speed of light to start with, only making small adjustments en route to its destination, there's not much room for any countermeasures to be deployed in time to matter. By the time its seen, it's already right on target, and launching chaff or something wouldn't change that (or even be outside the hull by the time it impacts). A single rocket taking down a multi-billion dollar vessel? Seems perfectly cheap to me, even if the guidance systems were made by contractors and so ran into the tens of thousands of dollars per shot. If it hits, it hits, and if it hits hard enough to bring down the target, it's more than payed for itself.