I've often wondered if the USN has some sort of munitions for its submarine fleet to expend on large numbers of small boats. 4 Mk48 torps max at a time (8 with the 3 Seawolf I suppose) doesn't seem an efficient or cost effective way of picking off swarms of silly little boats with a couple of SRM on board. Does it? Yet as Sax said, in addition to the air power, the subs are the most forward deployed defensive unit in the entire CVN screen. Being the tip of the spear, I would hope they have a way of dealing with these threats directly, instead of just being an ISR platform to call in air strikes on them.
I think that a lot of these new swarming killer drone type things would have great potential for SSNs to hit large groups of smaller threats, instead of wasting multi million dollar torps (overkill for a single crappy fast boat) on them, of which they can only really attack 4 at a time at most.
I've been watching a lot of vids of modern fighters dispensing munitions on life fire ranges. THere is some good footage of USMC Harriers operating of a Brit CV, attacking floating targets nearby with cannons and practice dumb bombs. Small boats would be in big trouble with a 4 ship of Harriers, much less Super Hornets dropping cluster munitions on them. These modern cluster and sensor fused weapons vs large groups of zippy speed boats would be ugly stuff for the guys on the boats. The only way I think they could even threaten the USN is when small single ships are in the regions/waters very close to Iran, but against a CVN group with 1 or 2 SSNs, 3 to 5 escort ships, maybe even the new LCS with a lot more missiles and other weapons, all far out to sea and a long range trip for any attacking Iranian Navy units - heh, good look with that Iran.
The ballistic and cruise missiles are another matter, but again, the new radars and missiles already here and those coming soon seem to be a very could counter to these threats.
I don't think the CVN groups will be outmoded or going anywhere soon, IMO.