Phalanx doesn't work tho' :-) In 1991 Iraqi forces launched a Silkworm missile against USS Missouri. The ship launched decoys... and its Phalanx guns promptly targeted those decoys. Fortunately there was a Royal Navy ship, HMS Gloucester, in the vicinity which dealt with the problem with a good British weapon, the Sea Dart missile. This was the first real "drone on drone" combat, if you will.
Will this capability exist? Yes, probably.
Am I concerned that this capability will be deployed against me? No, not really. Theoretically it could, but then again, so could a dude with a gun. I live in a democratic first-world country, the capabilities of my own government are likely to exceed the capabilities of those who want to kill me. And theoretically maybe my government might want to kill me... but it could already do that anyway, using a dude with a gun.
For now. Things change.