How to disable Safari's Frequently Visited blacklist on macOS?
I don't know whether there is a blacklisting mechanism.
I think that if you ever delete a site from the frequently visited window, then it'll never appear again:
Check BannedURLStrings in ~/Library/Safari/TopSites.plist with
/usr/libexec/PlistBuddy -c print ~/Library/Safari/TopSites.plist