There really aren't that many authorship debates, since an author's name will usually become associated with a story whether or not they actually wrote the work in question --- such as Homer (leading to the Homeric Question) or Aesop --- and with the invention of the printing press, they'd usually get their names on the cover to boot. Pretty much the only way we find out about authorship controversies is if those debates themselves enter the historical record, such as with Alonso Fernández de Avellaneda; lacking further evidence, we might have come to the conclusion that de Avellaneda was a real person. Wikipedia lists all of twelve authorship debates, none of which appear in Jasper Fforde's books except for the Shakespeare authorship debate. So I think the answer to your question is no, no other debates over historical authorship over literary works are referenced in the Thursday Next series.
The question of the existence of certain works is an interesting one for the Thursday Next series, given that one of the books in that series, The Great Samuel Pepys Fiasco, doesn't actually exist! Looking through Wikipedia's list of literary forgeries, I don't see anything mentioned by Fforde, even such famous frauds as Ern Malley, but there's probably some in there I don't remember or haven't connected with fraud specifically. I'd love to know if anybody thinks of others!