PS. Just found Semantic MediaWiki which looks very interesting.
Yes, this could indeed be a nice use case for this extension. It gives you some more freedom for describing relationships between your articles, and maybe there are also other properties that one could associate with some compounds (e.g. molecular mass).
Easy export of RDF is one obvious advange, but I'm not sure what other benefits there are of using the extension. Here is an example of any entry (no taxonomic information is shown): http://www.humancell.org/index.php/CHEBI15334
If the taxonomy is all that you need, categories could also be a sufficient solution -- the displayed article names really seem to be your only problem here. Would it help to create redirects between articles with nice names and articles with ugly names (note that you would also have to use "plus" for "+" etc.)? If the category mechanism is used only for browsing, then this might already suffice.
I agree, I had thought of using redirects too and I think this is the way to go.