Historically, neither USN or IJN flattops had armored decks (Brit CVs did, but it reduced the number of A/C it could carry compared with other nations' CV of comparable displacement). I do wonder if ships in AH model armor (in the way that tanks are modeled), or if the software just adds up total weight of ordnance (i.e. can you sink the cruiser with your side-arm, if you shoot it a zillion times?). A BB typically has waterline belt armor and main gun turret front face armor that is roughly equivalent to the diameter of the main guns (a rule of thumb), while the deck plating is some fraction of that. So a close range shot with a given calibre of armor-piercing shell to the side of the hull doesn't penetrate, but a long-range plunging shell of the same size might easily penetrate the deck armor.