Yamamoto's radio traffic was constantly being monitored, and his flight plan was intercepted re times, where, and other data.
There was a fierce debate on revealing this or not. It was hand carried to FDR. He slept on it, and he said to take Yamamoto out. The danger of doing this, could have signaled the Japanese code people that their code had been intercepted, and big changes could have been instituted after Yamamoto was intercepted and killed.
The plan was drawn up and acted on. Yamamoto died as a result. Outside of some minor code changes, nothing radical was done on their end. Many still argue that we should have left Yamamoto alive to crack his coded messages to really hammer the Japanese in all of their future Naval operations. Like all things that happen in war, there are two sides. Killing Yamamoto was a pschological victory for our side and a devastating one for the Japanese.
An excellent discussion of the intelligence war in the Pacific Theater is John Prados' Combined Fleet Decoded, recently reprinted in trade paper by the US Naval Institute Press.