I've been dealing with this for several days (had tried several recommended troubleshooting methods) and the only thing that ultimately worked for me was this https://matthewcassinelli.com/how-to-fix-recents-finder-macos-ventura-spotlight-index-terminal/
When I would try to reindex spotlight in the past, it was only taking 5 - 10 minutes. This process seem to do a more complete "reset" and now Alfred is picking up my Setapp applications again. As a side note, running "Rebuild macOS Metadata" from the Alfred preferences would give me an error about user being null on Ventura 13.0.1