The original plan for the attack on Pearl Harbor did not include a third wave. There was discussion about executing one, and the captains of the six Japanese carriers were willing to do it, but there were a few problems involved.

The biggest problem would have been time pressure. In the time it would have taken to rearm/refuel/repair the planes for the strike, get them up on deck and launch them, then get them to Pearl, execute the attack, then fly back to the carriers, the returning planes would have had to land at night. This wasn't something practiced by the Japanese pilots, and one could expect a fairly sizable number of losses as a result.

The second problem would have been increased American readiness. The majority of the Japanese losses came during the second wave of attacks, when the US anti-aircraft guns were up and running. Further, whatever US planes were still airworthy could be expected to be in the air.

The third problem is that Admiral Nagumo was concerned about the missing American carriers. For all he knew, they could have been barrelling down on him, deckloads of strike planes just itching to get within range. There was no way for him to know that the US had no idea where he was, other than "within aircraft range of Pearl Harbor."

As is, an argument has been made by author Alan Zimm in his book "Attack on Pearl Harbor: Strategy, Combat, Myths, Deceptions" that a strike on things like the tank farms would not have been as easy, nor as successful, as is generally thought.

(note: I am not personally a fan of Zimm's book, but he does raise a number of good points in it)

Regarding the minisubs, memory suggests to me that Yamamoto did not want to include them in the initial attack on Pearl Harbor, but they were forced on him anyway. I want to say I read that in the book "First Shot" by John Craddock but I can't seem to find my copy to verify.