cv10 - given that the AI does not fortify, that is a somewhat low bar LOL but my practice is as yours: 4 to 8 6" batteries and at least one 12" battery for Manila Bay. In my last game that didn't stop the surprise attack (I lost CA Cascade) but they crippled a Japanese B, worked over a CL and sank a DD or two, My second CA was torpedoed but survived and my two CLs got out without a scratch, so not nearly as bad as it could have been.
True, the fortifications only prevent outright seizure of the naval base - which is certainly worth doing, but not sufficient to defend the island. The primary purpose of fortifications is to enable a small group of men to delay a larger force, enabling a concentration elsewhere.
I can only assume that my USA player is more foresighted (or paranoid) and has a good-sized, well-trained Filipino army waiting behind the beaches.