I know for instance the Overdrive Link plugin saves the "manage discovered books" list in the db, but that is a per-library setting and makes sense that it should be there, not in calibre config.
In any event, the important thing is to avoid using hard-coded paths when you move the calibre config data. The databases on the other hand were built from the ground up to be movable and not dependant on a specific location in the filesystem. I am not aware that any plugin tries to mess this up -- they either store their config in %APPDATA%\calibre\plugins\mypluginconfig.json or else as specific types of info associated with a book.
Overdrive Link has manage found books, which is just a list of titles and overdrive weblinks,
Goodreads sync has info about your account in the json, and adds identifier metadata to the db,
Annotations saves stuff as a comment in a custom column plus json stuff,
plus other plugins I either don't use or don't have the patience to enumerate,
and I'm pretty sure they could ALWAYS do that.
The moral of the story is: don't worry, it's safe.
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