from what i understand smoking was not the issue with the color change. its sunlight. the plastic used on the SNES contained Bromine. this is what changed the nice grey color to the stained yellow color.
nice to see yours has little of this. the one i picked up was kept in a garage and is stopless on the ourside. sadly there is rust on the internal plate and the outside of the pin reader.
Yeah, the yellowing on the controller ports is almost certainly the result of that. It was thankfully kept in a relatively dark place most of the time, even when I was a kid, so that probably helped a lot, though I've seen comments that oxidization plays a role, too.
The nicotine is mostly the nasty, sticky crap I spent a couple hours wiping off, along with hardened human hand sweat (seriously, the PS1 controller was enough to make a person throw up and took an hour on its own) from my Mom's ex, and other sundry bits. Didn't cause the same kind of yellowing, but there was a definite veneer of something foul that darkened the color on everything. I think I got most of it, or as much as I could without dipping everything in a solution of some kind.