That's not so odd. Many WWII subs, on which the Civ5 sub seems modeled, had a deck gun with a bore in the five-inch range. In the early days of WWII the Axis' doctrine was to cripple a ship with a torpedo hit and then surface to actually sink it using the deck gun.
In 1942, the Japanese submarine I-17 actually shelled (To little effect) an ocean side oil field in California's Ventura County.