I'm having the same issue ever since upgrading to Alfred4
For me, it seems mainly to be Apple's apps that aren't showing up in the index...
Safari, Pages, Keynote and Numbers are fine.
But Terminal, Activity Monitor, Music, Photos, PhotoBooth, Quicktime, etc... no luck. Did apple lock them down somehow, or move them... or ?
Also... I notice that under Security and Privacy - "Automation", Alfred 3 is still showing up, but Alfred 4 is not... and there's no+- button to add it manually.