Yes , Japanese Army decoded US Army M-209 cipher but too late.It was few days before the end of the war.

(source:Tragedy of information defunct national by Eizo Hori pub1996)

Yes.

The Germans broke most of the British naval codes and were reading naval communiques consistently till early 1943, when the British realized and overhauled their system. In fact codes like naval cyphers 2 and 3 were changed monthly. Is the Germans had to break them again and again. On average it took the Germans 10 days to rebreak 2 and 3. The merchant BAMS cypher was also cracked pre-war and provided vital routing information for U-Boats for the first half of the war. The Germans also broke the US Army's mechanical encoder M209. But it was widely expected to be relatively insecure. So it was used mainly for local tactical information that only needed to be secure for hours or a day or two at most.

The Japanese received the BAMS code from the Germans. And it proved important in the first year in the Pacific. Not only was it used by British and Commonwealth merchants, it was also used by US merchants when communicating with the Commonwealth countries. So the Japanese had a pretty good picture of merchant shipping throughout the Pacific. The Japanese also proved adept at breaking US diplomatic codes. And during the war the broke Brown, Grey, and Black. Actually both the IJA and the IJN independently broke Brown... and never told each other. They also broke the State Department version of M-38. But not the far more critical Navy version. In general the Japanese seemed to have a hard time breaking US military codes. They never got a significant Navy code. And they only broke the relatively insecure M209 near the end of the war.