They obvoiusly have super brains if they can learn to do as much as they can with chakra - Amegakure had skyscrappers.Stop referring Naruto as the real deal it's fiction. Kishi made a mistake there. You can't just possibly learn to build skyscapers in less than 10years it's in Illogical!
And yes they are Super-humans but they don't have Super-brains!
They know Ninjutsu,Genjutsu,nature elements etc + already had buildings before,and even skyscrappers - and Amegakure,and had different technology stuff.... Rly?
What if in some fairy tale like Lord of the Rings, Gandalf suddenly pulled out a Nuclear-fusion-powered Rail-gun, and nuked Sauron from Orbit... What would you say? "Oh, there is magic there. So it was just magically brought into existence. Totally makes sense!" <--- This is how you sound to me.
Don't you think Shinobi coudl learn how to make buildings?