It has come to light that the original logo in 2004 was a Koffing with a Swastika instead of the normal crossbones thing
https://www.youtube.com/watch?v=lPG6vIN8Kx8
Video by cecilily - We need to talk about the Nazi past of Smogon
This is so outrageous it seems fake, but they adressed it last year and decided not to change the name which is peak 
What happened more than likely is one of two things, early internet edginess, or the person paying for the site at the start did the thing that a lot of forum owners did back then "it's my forum, and I can do what I want with it".
I can't find the energy to get worked up over this in either case, mostly because there's bigger fish to fry in the grand scheme of things, and both cases were pretty common in early internet especially the latter which is where the unofficial rule 0 of forum posting comes from, don't piss off the guy paying for it.