I did read this on Reddit (don’t worry, I took a shower afterwards):
The real reason is the charming one- namely that Gene Roddenberry had a friend (a radioman, as I recall) during WWII named Kim Noonien Wanh. Gene lost contact with his friend and apparently had some hope that tossing the name in there would draw the ear to a television and maybe he’d find him again.
It was Korea, not WW2, but the rest is kind of sweet.