I believe the devs confused these gunboats with accounts of US sub encountering "converted gunboats." While I can't find an view of a specific wartime Japanese example, here is a US converted gunboat from between the world wars:
Her upper decks had been removed to increase open water stability. A variety of different ships were converted to gunboat status during the war. Steamships were common.
The gunboats in the game should probably be excised entirely. Both the
Atami and the
Hira were not part of the Combined Fleet, but rather assigned to the Japanese naval forces in China, as can be seen in this document:
http://www.ibiblio.org/pha/pha/misc/45-41.html
They and their sisters (
Atami class: Atami, Futami; Seta class: Seta, Katata, Hira, Hozu) were Yangtze River patrol boats. To show where they where later in the war, references indicate that the
Atami was damaged by Chinese aircraft near Tung Ting Lake in China on June 10, 1943, while the
Hira was damaged in an air attack at Kiukiang, China in August of 1944.
At the most, they might appear occasionally in Shanghai harbor.
Here are some examples of converted gunboats sunk by US submarines:
SHOSEI MARU
Japanese Navy; 1929; Amagasaki Zosensho; 998 tons; 210 x
30-5x18-7; triple-expansion engines.
The steamship Shosei Maru was taken over by the Japanese Navy
for use as an auxiliary gunboat. On May 20th, 1944, she was torpedoed
and sunk by a U.S. submarine [U.S.S. Silversides] about 50 miles S.W. of
Guam.
NIKKAI MARU
Nissan Kisen K.K.; 1938; Uraga Dock Co.; 2,562 tons; 297-9 x
45x23-8; 201 n.h.p.; compound engines & L.P. turbine. The
steamship Nikkai Maru was taken over by the Japanese Navy and
converted into an auxiliary gunboat. On November 26th, 1943, she
was torpedoed and sunk by the U.S. submarine Ray 350 miles N. of
the Admiralty Islands.
KEIKO MARU
Osaka Shosen K.K.; 1938; Uraga Dock Co.; 2,929 tons;
297 -9x45x23-8; 255 n.h.p.; compound engines & L.P. turbine.
The steamship Keiko Maru was taken over by the Japanese Navy
and converted into an auxiliary gunboat. On November 8th, 1942,
she was torpedoed and sunk by the U.S. submarine Seawolf off Mindanao Island, Philippines.