Natural selection imo. There are bound to be those that are not necessarily smarter, but just adapt better to the human presence and dangers that they face accordingly.
Is this story translated? If so can I have a link? Im more inclined to read fanfics that dont always talk about Reimu and Marisa's (A Youmu is fine too)
"What a shame... Marisa talked many times with that Marisa on the hunting grounds, but even though she was such an easy Yukkuri, this happened..."
"I'm sure Marisa understands too, myon. Yukkuris that think only of taking it easy are dangerous for the herd. And Yukkuris that want to make lots of little ones are just as bad for the herd as Remirya or Flandre, myon."
"I see... if there are too many little ones, there is no way we could hide from mister humans..."
"That's how it is. Now let's return to the herd, myon."Exiled Yukkuri - Wild Yukkyuri - First Part