I think it boils down to Occam’s Razor...what is most likely at first glance is usually correct.
To me, what is more likely:
1. A 30,000 ton sluggish cargo vessel transiting one Japanese port to another, somehow getting a plan together to arrange to have their vessel in the vicinity of US navy vessel (without knowing the exact mission or plan, even if you have eyes that can watch the vessel leave port) in a position where they can ram the vessel. Then, make the large, lumbering vessel perform really really unusual maneuvers that even under the worst of circumstances would attract the attention of an employer who clearly would be monitoring the vessel’s progress at all time, and do it in such a way they could corner and ram a specific vessel that could run circles around them, and probably would have men on watch at all times.
2. A civilian vessel on autopilot, manned by minimum watches in the wee hours of the morning, with the lone bored crewman on the bridge surfing porn or reading a book, not paying attention in the least, and a US Destroyer traveling at an oblique angle towards the civilian vessel though in the same direction, where all the watches on the US Navy ship know that the OOD (some LTJG or LT) knows about it because they were probably informed by the bridge that there was a ship off the starboard bow traveling in the same direction, and in the night, the two ships crept closer and closer, someone wasn’t watching the distance or misjudged it. The junior officer standing watch may have thought “Should I wake up the Captain?” as the others on the bridge eyed him, and when he decided against waking the Captain (who wants to get chewed out for no good reason?) everyone relaxed, because the OOD was managing the situation until someone said “Sir, she is getting much closer!” followed by “Well, let me know if she gets within 2500 yards” from the OOD who thinks “That is what the Captain told me”, only to be followed by “ Sir, she is at HOLY CRAP!” and “HARD PORT!” from the OOD as he looks over.
To me, the first one is just improbable (not impossible, after 9/11) but improbable.
The second, that one is as old as the sea.
That makes more sense, I agree.
The only thing I might add is that if there was a CPA-zero situation, the quarter master, lookouts, and the CIC surface watches should've all been echoing the same thing to the OOD. All of these reports about this contact should be entered in log books, along with any action take by the OOD.
#2 is probably the most realistic description of the of events. Posted by someone that has been there and done that.