The SS 393 insignia.

US Sub WWII  Surface Armament

The SSN 651 insignia.

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 During the course of WWII there were 10 different classes of subs fighting for the US. Starting with S Class, Argonaut, Narwahl Class, Dolphin, P class, Salmon/Sargo class, Tambor class, Gato Class, then later the Balao class.
There were basically two types of "defensive" armaments on these boats.

Small bore automatic weapons:

 Starting with 50MM water cooled machine guns, they were found to be impractical. It was cumbersome, took too long to set up, and the cooling system would clog up with sea salts. The next move was to Swiss designed 20mm / 70caliber Oerlikon. They worked well at first as anti-aircraft and small craft defense. As aircraft got faster the Oerlikon became useless for anti-aircraft. 

A 40mm/70cal Bofors is on the after cigarette deck (left) and a 20mm/70cal Oerlikon is on the forward cigarette deck (right) of the USS Pompanito SS383. Ammunition storage lockers are underneath the cigarette decks.

The Bofors company in Sweden had been working on an improvement to a German design 56mm gun from Krupp Iron works. Unknown to the Germans who owned 1/3 of Bofors, they were working with the US government on a new 40mm rapid-fire version of the weapon. The design was accepted, and a license to manufacture the gun was given to the U.S., Great Britain, and Canada.

The Bofors 40mm anti-aircraft gun not was not only popular with the U.S. and it's Allies, it was also used by the Germans, and Japanese.

A single mount 40mm/70cal was adapted for submarine use, and replaced many of the 20mm/70 Oerlikon guns. They were used for air defense and to attack sampans and other small craft of the enemy. Most boats also had stanchions along the perimeter of the boat, where portable 50mm air-cooled machine guns* could be used.   *Refers to the Browning M2 .50cal hb machine gun

An explanation of the caliber designations of the 20mm/70cal and 40mm/70cal guns can be found here.

The other type of armament were Deck guns and you can find out more here.

 

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