The third strike was not really an option.
Japanese doctrine did not emphasize attacks on infrastructure. The Japanese also did not have enough aircraft or ordinance to effectively damage Pearl Harbor as a fleet base. The fuel tanks were protected enough that a fire in one would not normally spread to other tanks.
Nagumo was also running low on fuel, particularly for his destroyers, He could not afford to hang around.
Remember, Pearl Harbor was a diversion, designed to slow the US down. The Japanese target was the oil fields and infrastructure of the Dutch East Indies.
Welcome to the Canteen, GreenLanternCorps...and thanks for the added information.