Was the Pearl Harbor attack detected before it happened?

MIA Pearl Harbor 

As a social historian and a lover of mysteries, one aspect of the attack on Pearl Harbour intrigues me more than anything else.

This fact is the disappearance of a Naval Lieutenant days before the attack.

The officer was known for his long mountain walks; he reported to the sick bay two weeks before the attack with a broken collar and a fractured wrist. 

While he was off-duty sick, one day, he took another of his walks, this time, he did not return, and to this day, the body has not been found,

The most common supposition is he fell off a cliff and died from his injuries; this does not explain the non-appearance of his body.

Another possibility is that he came across a Japanese spotter base days before the attack and was killed to conceal the events of December 7th, 1941.

Some people would say the USA fired the first torpedo of the war in the Pacific by sinking a Japanese submarine close to the harbor, but the question is, what was a submarine doing that close to the naval base without announcing its presence to the base; as at that time, the war with Japan had not begun.

My opinion has always been, and will remain so, the timing of the message telling of the start of the war was not a case of bad timing; the Japanese know of the timeline you cross and the hours you gain.

One thing that intrigues me is if their intelligence was so good, why did they not know half of the fleet was out of the base on exercise?