How a game is "supposed to look" is certainly up for debate. I happen to think that S-Video and up often ruins some intended visual effects on certain Genesis games where the designers counted on some blurring to happen to squeeze out some additional colors/effects. Of course, to counter that, there's also the simple fact that games overall do look better when you start moving past composite. It's one of the reasons why I sort of hedge the difference and opt to use the best natively available output on my consoles (when practical) but never mod them to use unintended ones. It's somewhat arbitrary, I know. But I like to get the best out of my consoles as I can while at the same time remain committed to an "authentic" experience that is as close as possible to what was originally intended. It's a work in progress philosophy.
That being said, I've never really had this issue with Super Nintendo. I don't remember ever seeing anything on the system that looks as if it's aesthetic design counts on bleeding or blurriness.
In the realm of emulators, I figure the argument is much the same. There's really no difference between saying an emulator looks "weird" on a certain display and saying a SNES looks "weird" on the same display via S-Video or something. But even if it does look weird, unfortunately the NTSC filters that are supposed to make emulators look like they're displaying on an old CRT end up just looking strange and awful.