But we still put people on planes.
The unsettling difference, that you hit on, is: when Fujita finally got through to the FAA, planes and pilots were quickly brought up to speed; but the sea transport industry has seen the rogue wave research and doesn't seem to be particularly interested in changing anything.
The cost of "prepared against" matters as does the value of X.
Some risks are worth protecting against while others aren't. While the right answer for a given risk may change over time, the latter group is never empty.
Of course, you may value your safety differently than the folks making that call for ships. If so, ....
... keeping in mind that these ships are most likely shipping containers, and that all things involved are likely covered by some insurance policy that has evolved over hundreds of years of industrial experience (where rogue waves need not be known or even measured to be a factor). I don't think it's too unreasonable to carry on regardless, however misguided. I've always found it strange though.... especially since I've always wanted to do the banana boat "cruise" thing!
The solution probably isn't better ships, but better mapping of wave conditions and routing around more dangerous areas.
If I climb on a ship and you tell me "well, there's a 1 in 100'000 chance that we'll be hit by a freak wave and then it's quite likely that everyone on board will die, since the ship will be broken in half and sink", that's a very different thing to say than "well, there's a 1 in 100'000 chance that we'll be hit by a freak wave, and then the ship will sustain severe damage but should be able to limp back to shore or at least float long enough for a rescue."
The difference between those two scenarios is probably less expensive than you think.
1) Ships are built to withstand normal waves, and have a high likelihood of sinking if hit by a rogue wave.
2) Rogue waves are a regular feature of the ocean, frequent enough that a number of ships every year will be hit by rogue waves.
3) These rogue waves can effectively occur anywhere in the ocean.
4) Despite this, commercial liners, cruise ships, tankers, etc, continue to go out to sea, taking sometimes hundreds of people with them.
Is this basically saying that this common mode of transportation is inherently unsafe and to be avoided? It's one thing to say that "shit happens, and if something goes wrong with the plane, you're fucked", and another altogether to say "we know that this will happen, for sure, one out of X times, no matter how well we may prepare, and it will most likely sink the ship". X may be rather large, but the point is it could be prepared against, but it's not.