History: Pearl Harbor Bombing

Striking the Pacific Fleet at anchor in Pearl Harbor carried two distinct disadvantages: the targeted ships would be in very shallow water, so it would be relatively easy to salvage and possibly repair them; and most of the crews would survive the attack, since many would be on shore leave or would be rescued from the harbor. A further important disadvantage—this of timing, and known to the Japanese—was the absence from Pearl Harbor of all three of the U.S. Pacific Fleet's aircraft carriers (Enterprise, Lexington, and Saratoga). Ironically, the IJN top command was so imbued with Admiral Mahan's "decisive battle" doctrine—especially that of destroying the maximum number of battleships—that, despite these concerns, Yamamoto decided to press ahead.
Japanese confidence in their ability to achieve a short, victorious war also meant other targets in the harbor, especially the navy yard, oil tank farms, and submarine base, could safely be ignored, since—by their thinking—the war would be over before the influence of these facilities would be felt.