Cruiser and battleship missiles are actually threatening to their main targets - capital ships. They are not designed to be used against fighters, so it's perfectly balanced that they don't work against fighters.
It makes perfect sense for gunboats to have anti fighter/bomber missiles, as they are anti fighter/bomber ships. Cruiser and battleship missiles on the other hand are anti capital, as cruisers and battleships are anti capital.
It's not 4.84 anymore, the balance system has changed and some weapons are completely different now. Cruiser/Battleship missiles are one type which have been completely overhauled.