Nintendo has an established policy of being very opaque regarding their pursuit of copyright claims. Their stated company line is that they never grant permission for anything outside Fair Use or officially licensed materials, but they clearly do allow the maintenance of unlicensed fan websites which do go beyond Fair Use, of which Smogon is almost certainly an example. For whatever reason, the company is not inclined to elaborate on its reasoning.
This said, there are options available to us. The words Koffing and Smogon are not registered as typed or standard character drawing trademarks in the United States. While Nintendo of course has claims to its intellectual property on a variety of grounds, it has registered as trademarks only certain particularly significant names, such as Pikachu, Togepi, and Meowth. The legal ramifications of this are of course complex. I can elaborate if necessary, but:
I don't want to waste my time with redundant research. If the site staff wants me to prepare a formal memo on merchandising options, I can do it, but it is not a trivial project.