Ctrl-X in Nano is arguably more nonsensical, considering that vi was made in an era long (decades) before many of the conventions we know today came about. They were figuring it out in real time. And the criterium here is much simpler: it must be available on all keyboards so no fancy keys. That's all.

On the other hand, when nano decided to use Ctrl+X for eXit, Apples Ctrl+X/C/V had already been brought over to Windows and Apple, and was also the de facto way for most Linux apps to handle these inputs although I do think it came before any "official" efforts to standardize these shortcuts in desktop environments.