The symptom was that mail.app search always returned 0 results when searching, but spotlight did find results.
What I needed to do to get it working again was to set:
sudo defaults write /Library/Preferences/com.apple.security.appsandbox UnrestrictSpotlightContainerScope -bool false
then reboot
and then run
sudo defaults write /Library/Preferences/com.apple.security.appsandbox UnrestrictSpotlightContainerScope -bool true
reboot again and voilà, I had working search again.
Update:
Turns out killing mds in activity monitor does the job fine as well. 🤦🏻♂️