For starters, Wind Waker and Twilight Princess happen in two completely separate timelines. Wind Waker happens in the adult timeline (I think) and Twilight Princess takes place in the child timeline. Side by side, there's still a few hundred years of difference between Wind Waker and Twilight Princess.
In addition, when you were in Twilight Princess, when you looked up, did you see the City in the Sky? If you did, then I don't know what to tell you. If you didn't, then that is exactly why. The City in the Sky is far above Hyrule, almost into space if you take into consideration the required height for something that large to be illegible for the naked eye. The International Space Station is quite large as well, but you cannot see it from the ground with the naked eye (or a weak brand of telescope) due to the distance.
Now, that's all theory. In actuality, I believe the people down at Nintendo hadn't thought of it yet at that time.