Couple points.
There is no indication that stealthy FACs would ever be used in swarming attacks, they are better designed for covert strike. They are also very expensive and only available to certain nations.
Thinking about tactical and strategic use of motherships would imply they wouldn't be close to shore. The point for a mothership is to provide OTH standoff weapons support and OTH logistical support to smaller units deployed closer to shore. How many FACs would go off chasing motherships into blue water?
Well, I think incorporating OTH standoff weapons support into a mothership would be a design decision. I could just as easily see one who's sole purpose was OTH logistics and/or transport of smaller units and have let DDG/DD(X) provide the firepower.
I think a very valid concern exists with helicopter assault against FACs that are armed with certain AAW weapons. The 2003 Iraq War exposed that even the heaviest helicopters like the Apache are highly vulnerable to "wall of steel" gun attacks, the most likely defensive weapon in a large a swarm of FACs. Alternatives would be CH-130 gunships or A-10s, both land based US Air Force platforms.
The Apache vulnerability in OIF and Operation Anaconda was due to the decision to fly low-n-slow over enemy-held territory. This exposed them to all manner of 'trashfire' including AAA up to HMGs, RPGs, recoilless rifles and so on.
This wouldn't be the case with swarming FACs. Even stealthy ones could be detected at significant distances, and the number of targets would be orders of magnitude lower than during OIF/Anaconda (where a target might be one guy manning a DShK or packing an RPG).
Still, a 57mm or RAM launcher would pose a significant risk to a Helo launching Hellfires.
Helo-launched AShMs, OTOH, easily out-range anything short of a good-sized SAM. Targetting would have to be off board via BAMS GHawk, MMA or whatever.
So a question I would raise is what suitable countermeasure other than attack helicopters exists or could be deployed from a mothership to strike against heavily armed littoral FAC squadrons with FAC based AAW defenses?
Well, my guess fixed-wing NavAir would be employed first, if available.
Given that FACs have limited range and endurance, one could hit their ports and refueling points and just wait for them to run out of gas.
Personally, I'm less worried about large fleets of stealth FACs in our opponent's inventories than them using stolen or captured merchant vessels and other small civilian craft.
In crowded waters, we may have to search each ship and boat to determine friend from foe.