Because Pacific Fleet Headquarters wasn't in the same mental state of readiness as the captain and crew of the USS Ward.
No, they weren't. Just because "The Japanese carrier fleet has disappeared and we don't know where they are" is no reason to be on alert. After all, they were looking to the south and found just the small sub. Too bad the carrier fleet was to the north. Fortunately [luck?] the American Navy carriers were out of port or it would have been a short and most unsatisfactory war.