This is definitely a permissions issue, as I am experiencing the same thing. I do not know whether Apple has changed the authorization process/required permissions, but I'll add a pair of observations (which may or may not be obvious):
Alfred can still see all of my third-party, non App-Store-installed applications in my /Applications directory;
Running a `ls /Applications` command also shows only the aforementioned subset of the /Applications directory's contents, so my shell does not appear to have full permissions either!
Alfred does not appear in the Automation tab of the "Security" pane, but it does appear to be enabled in the "Full Disk Access", "Files and Folders", and "Contacts" panes on my system.