Factual error: The Nimitz's position is not indicated, but most probably it is somewhere south or southwest of Pearl Harbour. Similarly, it is not indicated where the Senator's boat is sailing, but it should be somewhere west or southwest of Pearl Harbour. The two Japanese Zeroes encounter the boat and strafe it, but their flight seems to indicate they would be headed toward Pearl Harbour (or at least some populated island surely) which would indicate they were headed north or northeast. If that were the case, they certainly flew in a large circle around the island chain, which seems unrealistic in terms of fuel, distance, and reconnaissance use. Also they would have had to have flown between the Nimitz and the pleasure craft then headed back toward Pearl Harbour, which makes even less sense in the movie.
Factual error: All the aircraft embarked onboard the USS Nimitz are part of Carrier Air Wing Eight, and carry the correct tail code 'AJ' for that wing. CVW-8 was Atlantic assigned, as was the Nimitz herself at that time. A Pacific based CVW uses the 'Nx' codes.
Answer: First, he had a look of concern for the young pilot under his command. Second, he is also confused as to what exactly happened. They believe it was a first strike weapon, that the world was ending.