In all my years of gameplay, no game has ever occupied so much of my time (in aggregate; I do take extended breaks from time to time) or caused me to shake my head in wonder as much as Order of Battle.
Here it is, eight years later, and we are still digging up bugs! And this one was another one of those really subtle jobs in which the investigator is thrown off the trail by the red herrings described above (albeit those being all true).
One thing always in mind about OOB editing is that there is ALWAYS a logical answer to an anomaly, barring a programming bug in the tools themselves. It was right there while I was preparing my post above and I still missed it. After reading your latest post, I had to do a playthrough, encounter the error, then return to the editor with sleeves rolled up, sweating brow, and madly staring eyes. And I did find it.
First, the playthrough. I nuked the campaign to Coral Sea, then johnconnored the Japs to immobility. I sailed my warships to find and sink only the two enemy fleet carriers. (Naturally, the randomiser had to place one of them all the way on the other side of the map.) That accomplished the secondary objective:

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Then I finished the scenario:

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The campaign gave me the appropriate message:

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But when I started Midway and lifted the FOW, there was the Japanese light carrier, both at Deployment and Turn 1:

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The trigger that was supposed to remove CVL Ryujo did not activate. Why?
Here is why. See the campaign variable specified in the Coral Sea scenario and in the Campaign Variable:

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Now look at it in the Midway scenario:

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Wrong variable name! In these Midway triggers, it should have been "coral_carriers_killed" to match the way it was set up in Coral Sea.
Eight years, Halvralf. Eight years it took to unearth this bug!
Thanks to you bringing it up, that is. Look, I will be honest two ways: 1) My opinion matters naught because I am not official and know next to nothing about the status of this game other than my own impressions, and 2) Those impressions tell me that this game is in mothballs and that the likelihood of this getting fixed in a future patch are nil. Heck, I have seen stuff pointed out in this manner and ignored in patches as they concentrated on things of their own interest, the latest being multiplayer mode.
So, if I were you, I would do what I have been doing, which is correcting the campaigns for such errors in my personal copies. At least you would know your own versions are working. (Caveat: should there be another patch, it will overwrite your edited copies so save them elsewhere).
In this case, in those two Midway triggers, change the campaign variable to "coral_carriers_killed" and consider making the changes in the text messages that I recommended in my previous post.