supplemental .zip files
In an attempt to move to Zotero entirely, I wonder whether a supplemental zip file that is accidentally expanded inside a (Mac) ~/Zotero/storage/ABCD4567 folder could break something. I would be careful to Show File in Finder and copy it elsewhere if I use it, but still would want to store it in Zotero with the publication.
If you really wanted it linked to Zotero somehow, you could store it elsewhere and add it as a linked file. Or, depending on what's in it, you could just unzip it and add the individual files as attachments, which would let you open them directly from Zotero.