The engine does not allow "variables" that can change, such as the time in port, once set, is static. The "Base Stop" objective doesn't really do anything, and there's no "over-nighting" with it. Changing the commando boat to a different vessel to launch is "stuck" once set, so you can't have a boat "launch" a raft one time, then change it to some other vehicle for the next, unless you change the boat (I'm really want to find a work-around to this). Making things "disappear" on a vessel is beyond my comprehension. That last bit - "beyond my comprehension" is a biggie...
- All of this affects the construction used for the campaign, so going up dead-end alleys has caused quite a bit of delay. Not being able to get the specialized boats to do their "specialty" looms large...
As for the IJN's Sen Toku that carried 3 planes, that was an unusual submersible, and would have been able to cause a bit of concern with the US war effort if the IJN would have had them sooner, but the US ASW (helped by having cracked the IJN codes), would have been able to at least eventually deal with those beasts. The Sen Taka however, was the streamlined, all welded hull, smaller boat capable of high speed underwater. It's numbers were "backwards" compared to other boats, in that it was faster submerged than it was surfaced, and capable of nearly 20 knots underwater for up to an hour at a time. Their "weakness" was they only carried 10 torpedoes.