Unfortunately that is exactly the case. Our sophisticated Navy was designed to fight other sophisticated Navies. There was a popular science fiction story several years back about a fighter pilot in an F-14 who was thrown back in time to World War I. It turned out that his sensors and weapons were completely useless against low tech fabric and wood technology of the time. Ultimately he figures out that he can damage them by flying close at supersonic speed but I digress. This is the same problem a Burke Class destroyer faces when it takes on a dingy.
I operated extensively north of that area near Socotra in the 1987-89 time frame aboard a Navy frigate. At the time were worried about Iranian suicide missions on small boats (boghammers) and in small private airplanes. Our radars could not pick out fiberglass boats from the surface clutter and we could not determine the intent of a small airplane and we had no weapons that were effective against these low tech threats. We were hell on wheels against Echo Class subs and Backfire bombers but completely flummoxed by those low tech threats. I believe the literature refers to this situation as asymmetrical warfare.
How did we counter this? We had to bring back the venerable M2 heavy machine gun. They came out of mothballs from the Naval Weapons Station in Crane IN and mounts were welded to the deck around the ship. Unfortunately the care and feeding of these Browning designed masterpieces had faded from corporate memory so they had to ask for volunteers of retired Gunners Mates (who responded en masse) to come and teach their successors how to set the timing and headspace. For the aircraft threat the Navy created Stinger detachments that would swap from ship to ship as needed with their gear.
I think the framework necessary for solving this problem exists. We also carried at various times what the US Coast Guard called "Tactical Law Enforcement Teams" (TACLET). This was when the government still pretended to care about the law and wanted to maintain the fiction that DOD was not violating Posse Comitatus in the War on Drugs. These teams of 5-7 petty officers and one junior officer would come aboard with their gear and weapons for as long as the mission dictated. Teams such as these are very effective and could ride ships through the pirate zone without any of the problems of arming crews or hiring contractors.
The only problem with this is that I have just solved a non-existent problem as they say. Why is that you ask? You see we don't have a Merchant Marine any more and thanks to blatant protectionism and union featherbedding we haven't for decades. When you sail the Indian Ocean a US flagged merchantman is a rarity of the highest order.
The only time a US flagged vessel is used is when there is no other way around the protectionist law. Maersk Alabama was delivering humanitarian aid under a US Government contract which specified that a US flag carrier deliver said aid, otherwise she would not have been within 2 or 3 thousand miles of there.
So this is technically not an American problem. The pirates probably won't get their hands on another American vessel because statistically there aren't any (and I am sure this figured into The One's calculus in allowing the action). This is a problem for the open registries like Panama and Liberia and I wish them all success in this endeavor.
You made some very interesting points. And your final analysis why Zero went along with killing the pirates if the scene showed the captain was in grave danger is probably correct as well.
I never heard of a story about an F14 back in WWI, but I did see "The Final Countdown" about the Nimitz going back to WWII - pre Pearl Harbor. I think someone did a study that the Nimitz could have taken out the entire Jap fleet, and the attack, in short order. It would have been shorter, but they [the planes] would have had to come back to re-arm.
As for steering clear of Somalia; easier said than done if you're transiting the Red Sea.