Structure info files for nether and end like Fortress.dat or Endcity.dat will not be created on a fresh server with default configuration without any plugins. Villages files seems a bit special, since villages_nether.dat and villages_end.dat will be created.

I tested flying around in overworld, nether and end. I came across a lot of structures and files like Stronghold.dat and Temple.dat where created successfully.

(I tried fixing the issue myself, but was without luck.)