What is meant by 'hiding' Kohelet or Mishlei? Who are those that wished to 'hide' it? How can a book have been hidden after it has been written? Is there any merit to my speculation that what is being discussed is the canonization of these sefarim and not their physical literary demise?
Very interesting question. The term "genizah" used is the gemara can mean that the books should be taken out of circulation. The reason given is the seemingly contradictrary passages. We find the term "genizah" used inreference to books that were not holy at all, such as in pesachim 56a the hiding of the "sefer refuah" (which was a book that had medical cures). So that could certainly be the discussion here.
However Avos d'Rabbi noson" 1:4 says "Originally they said Mishlei, Koheles and Shir Hashirim should be hidden, for they contain mere parables and they are not of the Scriptures. They hid them until the Great Assembly came and explained them."
Here the discussion is clearly if these books should be cannonized or not. It is unclear if the gemara in Shabbos is referring to the same instance.Firstly,it leaves Shir Hashirim off the list of books in question. Secondly, and perhaps more revealing, the reasons given are different. That seems to leave room to speculation that this gemara is not discussing the cannonization of the books, but rather if they should take them out of circulation although they were already canonized.
Prof. Shneur Zalman Leiman (of Kew Gardens Hills) wrote a book on the issue.
Be well, Moshe Rosenberg