First, I have to assume youkai are born from human fears. With your question, I think you are trying to induce someone into saying "youkai would be born in the outside world" which I do believe would happen. However, as I believe the outside world is dominated by a belief in science, people are far less probable to fear any unknowns, and more likely to want to find the answers to them. Since everything can be explained through equations and logic, there would be no reason to fear anything. Thus, no new youkai would ever be created.
The interesting part raised by everyone else is when you mix a logical society with part of an illogical one, or Gensokyo with the outside world. Say Yukari goes into the outside world and starts killing a lot of people. There would be no logical explanation for why and how Yukari can tear boundaries apart like paper. As she is powerful enough to overwhelm the most advanced war technology humans have (nuclear bombs), everyone would live in fear of Yukari. Then, in the blink of an eye, she leaves the outside world and goes back to Gensokyo, never to be seen again. People in the outside world still fear her... but their fears may become corrupted over time to create new youkai, which can then terrorize the outside world. Imagine a normal game of Telephone - by the end of the sequence, the original message gets distorted and has little resemblance to the original. Again, people will retaliate with nuclear bombs. If the bombs do the job, people believe in science. If the youkai are stronger than these bombs, people fear youkai.
The war between fiction and science can only be won by one side. Even in the real world, you can see the decreasing effect of religion (yes, I believe religion is fake) as people begin to believe in scientific theories. I believe ZUN is trying to mix the two worlds together, although he seems to be siding with fiction a lot more than science. The only thing I know about the Seihou project is the main character is a robot, so maybe the balance is inverted in those games.