Yeah, I don't think I saw anything missing. I saw the two analog sticks, buttons (possibly C-buttons from the N64) and D-Pad, along with the needed start (and select?) buttons, so everything seems to be in place.
Unless the L and R/ZL and ZR buttons are missing. In that case, yes, that will affect how the games are played quite greatly, because if Splatoon is going to be a thing for the Switch, then controls may need to be compromised to fit the necessary actions. But then again I could be wrong, and maybe I just didn't look hard enough on the controllers, and in reality they are in fact there.
Still though, it's just a hunch.