Interestingly the Taiyo Maru had been in Pearl Harbor on November 1-5, 1941 with IJN officers (disguised as civilians) on board to investigate the harbor for the midget submarines. The vessel arriving in Japan on November 17, 1941.
So the Taiyo Maru stayed in civilian service almost right up to the start of the war. Vessels that had already been requisitioned before the start of the war probably had priority for any armaments available. Also the ship would have had to been repainted and possibly had its interior at least partially redone to reduce fire hazard.
This lack of armament also seems to be the case with the Brazil Maru. There is a pic showing the vessel in the Spring of 1942 still sporting at least some of her civilian livery and no armament.