(It's one of the few emulators that can run PoP for TurboGrafx-16 / PC Engine, and it is also bundled with the legbop and lemdop level editors.)
I think I found out why.
It seems that D-Pad is always on the left side on the actual controllers, and Mednafen tries to emulate this.
As for why is D-Pad on the left, I found this: https://en.wikipedia.org/wiki/Talk:D-pad#direction_controller_for_left-handed_people.3F
Quite simple really. The right hand can press buttons faster than the left. Left hand is far better for steady button presses. That makes the right hand better for action buttons and the left hand better for motion control as motion doesn't need such rapid or precise changes in a binary control scheme. Placing action buttons in the left hand would just be making everything but movement harder.
The thought process was since games like Mario or Contra required more button pressing as opposed to say an Atari 2600 game.
The right hand is generally considered better for timed and reaction movements where as the left hand is considered better for broad, contextual movements.
But why are the buttons mapped to the numpad instead of some other letter keys?
Maybe someone thought that players would hold the keyboard like a game controller?
(And thus they must be mapped to keys on the right edge?)
Or they simply wanted to put them where it's more convenient for the right hand?
But then, people usually type (on the letter keys) with both hands, so I'm not sure this is why...