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 
Because it is peak white liberal performative nonsense to change the name. It's exactly what every white city dwelling liberal does when they find out something has a dark past, they change the offensive part (or do an overreaction, an example could be made for the prime directive in star trek) then pretend everything is still all hunky dory while doing effectively nothing material.
Maybe I've just had too many encounters with liberals who just never really cared at all to begin with to say that.
Yeah, the video mentions that multiple people are still around in leadership positions that were there during the time where that was a thing so you would probably hope to see some accountability from those individuals, In theory you could do that without changing the name and logo, but I feel like a lot of people will never look at it the same way after learning where it came from.
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.