whatis the difference between mounting holes and through holes?
When eagle generates Gerbers, holes end up as non-plated holes.  For a mounting hole, it's good when it's not plated.

Making non-plated holes requires an additional step in the fabrication process.  Some PCB fabs do non-plated holes as a part of their standard  service.  Some automatically convert non-plated holes into plated holes.  Some charge extra for non-plated holes.