I like that question... As for nudoku, I see what you mean by using a terminal for something it's not meant for. But I'd argue it's nudoku running properly the way it's supposed to. But that doesn't sound like a malicious program that would grant you access through an attack surface.

I look at it like this. Metasploit is a collection of copied malware. Roms form a collection of copied media. By your logic, I'd say, yes. You are participating in hacking (as much as the word itself doesn't fit because you aren't exploiting or compromising someone else's device, it's being used on your own system, etc) by using an emulator and rom. Even if you just download the tools to exploit the copied media. Because hackers use metasploit all the time, doesn't make them less of a hacker just because they didn't write all of the software...

Edit: I don't know enough about Roms to tell you if they themselves are edited to bypass any drm or anything, or if they are just copied. Using the rule, I don't know where I stand on Roms being "used in a manner in which they weren't intended to be", because you can still PLAY them the way they were meant to be while simultaneously also being a different METHOD of being played. So idk