I can speak to the US Navy in World War II.

Yes, there were a handful converted merchant ships with weaponry that was hidden. However, they were not generally used to protect convoys.

The US Navy was caught unprepared for the German U-boat offensive that was taking place off the East Coast in January/February 1942. The Americans had destroyers to escort convoys across the Atlantic, but did not yet have sufficient aircraft or smaller antisubmarine ships that eventually became ubiquitous during the war: wood-hulled submarine chasers and other patrol craft that were produced en masse for coastal areas. Convoys were still attacked and suffered losses during these early months, but dozens of ships that were traveling individually up and down the coast were easy pickings for German U-boats that stretched the limits of their operational ranges to cross the Atlantic. You can scroll down to see a map of ships damaged/sunk in January 1942 here (the U-Boats didn't begin operations off the east cost until mid-January) and in February here. The trend seemed to be worsening by March and April, by which time the Germans were surging U-boats into the area to take advantage of easy pickings.

According to Michael Gannon's "Operation Drumbeat," President Roosevelt broached the topic of "Q Ships" with Admirals Ernest King (then Commander in Chief of the US Fleet) and Harold Stark (then the Chief of Naval Operations, though King soon usurped this title and position) in late January, after the U-boat attacks had begun. According to Homer Hickam's "Torpedo Junction," it was King who mentioned the idea to Admiral Adolphus Andrews, then in command of the US Eastern Sea Frontier. King and Stark were aware that the Royal Navy had used Q Ships quite effectively in World War I and had begun using them again in 1939 and 1940, though with less success (I don't have much more information on World War I or the British Q Ships, unfortunately). Nevertheless, the President authorized $500,000 to convert a number of merchant ships to carry heavy armament and withstand submarine attack. The Navy spent $250,000 in February to procure the first three ships, steamers SS Carolyn and SS Evelyn and the trawler MS Wave. The funds seem to have been transferred to the ship owners and shipyards with little paper trail, trying to keep the project secret to preserve the element of surprise.

Q Ships would maintain the outward appearance of a merchant ship, but have several modifications and operate with a specific plan. The first alteration was to fill their holds with something that would maintain the ship's buoyancy after being struck by a torpedo, such as wood pulp, cork, or empty steel drums. The ships would also mount several naval guns on both side; the guns didn't need to be massive to punch a hole in a submarine pressure hull. The Carolyn and Evelyn, which were sisters, each mounted four 4" guns; two on each side hidden behind barriers, so that if a torpedo or shot from a submarine deck gun knocked one out, the other could keep firing. The Wave was smaller, and carried less armament. There were also hidden machine guns and some depth charges. The crew were volunteers from the Navy, wearing civilian clothing. The idea was that the U-boat should fire a torpedo that would hit the ship, at which point some designated members of the crew would scramble for life boats. The submarine would then surface (if it was underwater, many torpedo attacks were made on the surface) or otherwise close the distance to finish the "abandoned" ship off with its deck gun, rather than use another torpedo. At that point, the ship would drop the barriers hiding the weapons and have the U-boat vulnerable outgunned. The modifications were completed in mid-late March and renamed: Carolyn became USS Atik, Evelyn became USS Asterion, and Wave became USS Eagle, and put to sea on March 23. The ships were also given names of neutral-flagged ships to respond with if a U-boat challenged their identities via radio.

Atik successfully attracted the attention of U-123 just a few days later on the night of March 26/27. U-123 was a Type IXB U-boat that had been a part of the January attacks, then returned to France before redeploying back to the east coast in hopes of repeating her success there (she is also the main subject of Gannon's book). U-123 put a torpedo into Atik, which began the charade of abandoning ship. When U-123 closed in for the kill, Atik dropped her concealment and opened fire, but couldn't land a hit on the submarine. Machine gun fire did kill one German sailor, but U-123 escaped, submerged, and torpedoed Atik again. That was enough damage to sink her; the entire crew was lost. Asterion was nearby and tried to search for survivors but was unsuccessful. She had a relatively uneventful war, conducting other patrols but never getting the chance to spring her trap. Eagle also never saw any real action. A schooner, renamed USS Irene Forsyte, was converted in 1943 but also never found any U-boats. There was at least one Q Ship in the Pacific, but she never found success and was switched back to a cargo ship later in the war. The only other American Q Ship was an oiler named "Gulf Dawn" converted to become USS Big Horn. She did operate with convoys, but was never attacked by a U-boat. She had sonar equipment and was able to locate some U-boats, but postwar records showed that she never sank nor damaged any U-boats herself. In 1944, following the loss or retirement of the other Q Ships, she was converted back to an oiler and finished the war in the Pacific.

Q Ships had lost the element of surprise that they had in World War I, torpedoes and other submarine technology had improved, and other coastal patrol vessels and escorts begin arriving in summer and fall of 1942. Japanese submarines tended to focus their efforts on warships and supporting fleet operations anyway, making them of limited use in the Pacific. They did exist in the Second World War, but were mostly ineffective and not a large part of U-boat defense.

SOURCES

"Operation Drumbeat," by Michael Gannon, 1990

"Torpedo Junction," by Homer H. Hickam Jr., 1989

I haven't used this older source, but you might find some interesting details I haven't mentioned in it.