The 3rd Wave that was canned included provisions for the attack of much of the shore facilities of the base, while they were not completely spared in the first waves.

But the idea that Pearl Harbor was some sprawling base with multiple buildings of great import and their staffs keeping the fleet running isn't necessarily accurate for how the Pacific Fleet ran in December of 1941.

Admiral Kimmel was very much a sea going admiral. His flagship, the PENSYLVANIA was in Dry Dock #1 at the time, but for exercises, and in the vent of war the Operational Plans were for the CINCPACFLT to not remain desk bound in Pearl, but to be aboard his ships fighting them.

So for most purposes the shore structures were temporary housings for most, and Kimmel in particular enjoyed being at sea with the fleet.

This was not particularly unusual, Yamamoto for instance even when in port or at Truk rarely used anywhere but the Yamato as his office and flagship.

Nimitz then in a sense broke the mold, the task of rebuilding the fleet, and coordinating the now disparate Carrier Task Forces was what began the transition of the fleet staff towards a shore bound staff and formation.