Ok so in the game if your missiles go in to the water even if they haven't been launhced they won't work anymore.
They will "launch" but their power will be set to 0 I do believe.
So this means there has to be code for the to be disabeled after contact with water.

How about an xml option where you basically toggle if water disables the missile.
Something like "waterDisablesMissile = False" or something like that.

It would be great for submarine launched ballistic missiles (if your sub actually sinks)

(I guess you could consider this a little look in to the future, I was testing this exact thing so I would know if it would work or not, but I guess for now there will no submarine build by me)

uservoice link

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It will benefit most people, even IOS players bc you can ask somebody to xml mod the missile for you.