An "Independence Day" style salvo of thousands of tiny, EMP-hardened, possibly jet-turbine
We already have those. They're called "cruise missiles."
or even RTG powered drones with Mavic flight controllers and small bombs on them might be something of a pain in the ass for a carrier group to deal with
Oh. My. God. RTG powered drones? Have you considered the absolutely hideous power-to-weight ratio of RTG's? Not to mention the horrendous efficiency! For example, NASA's MHP-RTG weighs about 38kg and puts out only 157W...and 2400W of waste heat! Compare this to a Mavic's total weight of 743 grams. Truly, this is a terrible idea... ...which kinda flows with your entire concept. A swarm of such drones would be detected fairly easily. If you want to dispose of them at a distance, an airbust fragmentation warhead from a few SM-2 missiles would do the job. Closer in, CIWS or 5-inch airburst gunfire could, or perhaps even the new laser-based anti-drone system the Navy is already installing.
Even if a few made it through, there's not an awful lot a few drones carrying tiny payloads could do to a modern warship. Carriers have armored decks designed to resist 500-pound bombs, you know. Unless you have a drone carrying something substantially bigger, you're just going to piss off a battle group.
So...drone idea = stupid. You want to do any meaningful damage? You mount a 1000kg warhead on a missile that flies at Mach 3+ and swarm air-launch them...which oddly enough is exactly what the Russians came up with during the Cold War to threaten carrier groups and exactly what the Chinese already have.