No argument here. The KdB carriers already had torpedoes for shallow waters. Hitting the doors for the drydocks would have added thousands of miles (round-trip) for any potential battle-damaged ships as they would have had to go to Bremerton or San Diego. And as noted above, the presence of repair ships in PH also meant that the base itself was able to reconstitute quicker, perhaps. I hadn't given much thought to cranes, but that's a good point as well. they're needed to lift and remove armor-plate, turrets, etc, and without them -- especially with drydocks that must themselves be repaired -- it further turns PH less effective and would slow down things like repairing Yorktown for Midway and so on.
Lots of knock-on effects from your point here.
Neosho, near California on the morning of the attack, was a mighty valuable target as one of the few fast fleet oilers in PacFleet. A lucky, random hit on her here could have compromised the American response to Operation MO, to present another example.
So yeah, the hypothetical about attacking the tank-farms seems interesting, but other infrastructure or targets as well presented bottlenecks that might have hamstrung the Americans for a while.
I think the idea of putting the docks out of action with bombs and torpedoes hugely underestimates the problem.
In Dec 1941 PH had two operational dry docks, with another two under construction (a small destroyer sized dock completed in 1942 and a huge one in 1943. Putting dry docks out of action for any length of time isn't easy.
The dock doors were large hollow floating steel caissons, which were towed out of the way to open the dock entrance. They were fairly deep and strongly constructed to withstand the pressure of the water they were required to hold back. Think about how a Battleship TDS would operate to absorb the explosion of a torpedo warhead. Relatively easy to repair if torpedoed or to have new ones built with the Dockyard facilities available.
Look at what it took to destroy the similarly constructed dock gate at St Nazaire in 1942 (a target about 160' wide). Rammed by the 1,200 ton destroyer HMS Campbeltown travelling at 19 knots, the gate held until the 4 ton Amatol charge exploded. Commandos were needed to ensure the destruction of the dock machinery.
DD No 1 contained Pennsylvania, Cassin & Downes. The dock gate itself presented a target about 130' wide, a lot less than the c600' of one of the old Battleships targeted historically. On top of that there would have been no clear run in to it as Helena and Oglala were double berthed further along the quayside, as was the submarine Cachalot. Pennsylvania vacated the DD on 12 Dec.
DD No 2 was empty but would represent a target only c150' wide. On top of that it had provision for an intermediate caisson to divide it in half, which would have allowed at least partial use.
If you really want to disable a dry dock then the pump houses represent a better target. They control the inflow and outflow of water. Problem is they represent an even smaller target for a bomber, and often much of the machinery is buried under concrete in the dock walls themselves. Hence the Commandos at St Nazaire.
There was also at least one floating dry dock present, itself seemingly well sheltered from torpedo attack. YFD-2 contained the destroyer Shaw on 7 Dec 1941. Shaw was bombed and had her forward magazine exploded, damaging the dock itself. However, after being patched up, it was pumped out again on 9 Jan 1942 and was back in service again by May.