As establish in the setting, old, traditional Youkai retreated into Gensokyo because the outside world of science have drive away the mystic of the dark, so they have to go or they will die. But it's not like Youkai can't survive within the modern world, as example by Mamizou.
...Beside, I'm not talking about them anyway. In my opinion, darkness doesn't go away. As we tried to answer more thing, even more question popped up in it place. As the world become influenced by science, we find even more darkness within it, and within the society that it form. From the dark web to corporation, conspiracy and urban legend that have been abstracted by the ignorance...what kind of Youkai could you think popped up in those place, as an "easy" explanation to the massed?
Ex: Stock Market Youkai - Youkai that lurk in the digital stock market of the world. They messed with the price of the Market nilly willy, almost like fairy. There's no rhyme or reason, except to spread chaos for their own amusement. Based on the abstract nature of the economy, they grow on the ignorance of it, being the unknown that govern the everyday life.