It needn't be constrained to SAM batteries. For later ship classes like destroyers, battleships, etc., a general AA ability be given.
And perhaps it needn't be hard to implement. Perhaps AA could be identified in code to be some given percentage (20-30%) of a ship's attack or bombardmentment value. This value could then be applied against attacking aircraft to cause one of three possibilities:
1) AA attack fails, air strike resolved as is present (with chance of ship unit loss if damaged enough)
2) AA attack fails to damage aircraft unit, but causes it to abort strike.
3) AA attack damages aircraft unit, and also causes it to abort.
And alternately for the AEGIS cruiser, these could have inbuilt SAM capacity.
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