My recommendation is to have ships target offensive planes during defensive battles (maybe 15% chance to take down one 1 plane). Also, ships should be able to thwart incoming missiles and nuclear about 5% chance.
In offensive battles, ships could have a 5% chance to destroy tanks and kill soldiers (just 0.05% or 0.1% of the total Ground Force) when targeting infrastructures. This will make ships a more viable asset to choose from and maybe add to the complexity of the game.
But in order to do so a specific War policy is required to activate these perks.
Maybe this can compensate for its expensive price.