Safari tends to hold references to some items in RAM. (cache cookies, databases/localStorage, and History). Cookie does in fact remove them from disk, but Safari still thinks they are there.
you can test this your self by restarting Safari.
There is currently no way I know of forcing Safari, to update its internal references.
Those are Extension databases e.g.... (AdBlock, DoNotTrackMe, ClickToPlugin, etc...)
if you really want to delete them, you need to disable the option "Always Treat Browser Extensions as Favorites" on the Preferences Tab.