The Tamil Tigers are masters of small boat swarms, operating as many as 3 dozen boats ranging from 25ft to 65ft. It takes considerable ammunition to disable larger boats in small boat swarms, meaning the Mk15 would probably run out of ammunition in the fight.
I'm not sure how effective it would be against a small boat swarm. Against individual boats it would be extreamly effective, but against swarms there are still questions.
Your limited perspective of single ship in single operating environment is flawed, the LCS is a single ship in a series of ships.
When it is all said and done, the LCS will operate independently forward of the fleet the vast majority of its time in service, just like every other class of USN ship since WWII. Your statement would make sense if the LCS was going to fight WWII, but it isn't. Even if there was to be a WWIII against China, North Korea, or Iran the LCS would still be very deployable, just not as the main offensive asset you think it should be.