It's still not the same thing, though. Yes, Nintendo would have known that its own peripheral was in development, even though that peripheral would have begun development long after Kid Icarus development began (remember that Kid Icarus was originally supposed to launch alongside the system, before the Circle Pad was even announced).
However, there's a difference here. The third-party joystick controllers that you reference for fighting games aren't something that a game can actually even disable. They just plug in and they have the same buttons as a normal controller, but those buttons are placed differently and the analog joystick is shaped differently. Failing to exclude such hardware is not the same thing as specifically accommodating a circle-pad device that adds on from the side. Sakurai would have had to design the game to enable it--as part of a conscious design decision--and he explained quite clearly just why he chose not to do that.
The real issue here isn't the game, which was designed precisely as it should have been based on the hardware available. The real issue is the 3DS hardware itself, which should have included a second circle pad by default. I still wouldn't be surprised to see Nintendo rectify that issue, possibly at this year's E3 with an updated 3DS design. Unless that happens, though, including circle pad support for Kid Icarus is nowhere near the slam dunk win that some people suggest it would have been.
Let's not forget, by the way, that most players and critics alike find Kid Icarus to be a wonderful game and the control scheme is merely an annoyance that they're quite willing to tolerate. Since the bulk of the game was designed before the Circle Pad was even a possibility, it's also quite possible that the game balance would have been adversely affected by Circle Pad support and Sakurai wanted to maintain a consistent approach across various modes. There are a lot of things we might speculate about. My real point here is that his statements are both entirely reasonable and credible.
"Too often we enjoy the comfort of opinion without the discomfort of thought." - John F. Kennedy on reality
"What if everything you see is more than what you see--the person next to you is a warrior and the space that appears empty is a secret door to another world? What if something appears that shouldn't? You either dismiss it, or you accept that there is much more to the world than you think. Perhaps it really is a doorway, and if you choose to go inside, you'll find many unexpected things." - Shigeru Miyamoto on secret doors to another world