Frankly you really cannot balance this out. In point of fact, the carriers should probably not even be on the same table as the J/K's and with three carrier air groups, well the fight should be no contest. They tried to downplay the impact of carriers in the VaS book, my guess is they will be better performers in OOB.
Look, the grim reality of WWII is that airplanes are a major factor. You cannot, nor should you, make an effort to "balance" the game in this way. (one of the reasons WWI Naval Gaming is popular-its still about the ships!) Anyone who brings twelve J/K destroyers to a table with three aircraft carriers deserves the pasting he is going to get. Or, deserves the huge accolades they should get from winning. I chose the example because it creates a situation where the "unhittable" destroyers really have a minimal chance at victory.
Historical games, are notoriously difficult to balance, because you get wierd extremes. If you make it so that 12 J/K destroyers are the equivalent of three carriers, then you utter lose the "historical balance" of the game. Ultimately you are trading "tournament balance" for proper historical feel. Compromises will always be made, but the idea is not to create ACTA at sea.
One of the reasons sci-fi and fatasy games are so easy to make tournanment freindly is that the designers control the capabilities from scratch. This is not the case in historical gaming, where the desing parameters of your unit is preordained.
Now, add into this mix, the odd, and unusual and heroic, and historical gaming adds a whole new level of complexity in balance: how do you account for the sinking of the Hood or the incredible stand of the US destroyers at Samar during the Leyte gulf Battle. In point of fact much of military history is stories about people doing the things that, in theory, they should not beable to do. So based on historical performance, we get a slightly skewed vision of ship capability.
As players we want to count on our destroyers always dodging the main guns and getting in close to play hell with the battleships and cruisers. So the designers make it so that destroyers have a good chance at doing this, but in that process, create a tournament list that is "unbeatable." So now we are off to solve the destroyer issue in the name of balance.
In reality, the battle of Samar, would have gone differently 9 times out of ten. Its just that on that day, with those crews, the tin can navy rose above itself, and did the impossible.