Do you use web clipper frequently? If so each and every graphics element of a web page is captured and saved as a separate file in the "resources" folder.
I wonder if there's a limit on how many files you're allowed to store in certain public clouds such as Dropbox or OneDrive which Joplin can sync with. I remember a total number 100,000 files mentioned somewhere else in this forum, but I'm not sure if this a fact that can be documented anywhere.