Iff i understand it, no not necessary (and not adviced as they are kind of protected system folder).
Asuming you have to call js etc.. a basic folder in the root would be sufficient.
(mathjax seems to have it that way..eg rootfolder mathjax).
JS calls themself (just did a quick peek on Mathjax) CDN paths.. Those would need to be inside the theme php of theme you are using..
Since little is known (afaik) on incorporating MJ. one has to guess..
Mind! in regards to a previous post made earlier on adding LaTex> do NOT use Tinymce, but plain basic editor to be sure...
Hope this will help at least a little..