I found a way to let Alfred open aliases to applications (that is, .app directories). Funny, my use case was also to get Homebrew-installed Emacs to show up. As a result, these instructions are for Emacs, but they should generalize to any .app alias.
First, create a macOS alias, not a symlink:
In Finder, press Cmd-Shift-g and use Tab auto-complete to enter the path of the directory containing Emacs.app (In my case, it is currently /opt/homebrew/Cellar/emacs-mac/emacs-27.2-mac-8.3)
Press Cmd-n to open a new Finder window, then Cmd-Shift-a to go to /Applications
Create an alias by Cmd-Option dragging Emacs.app from the homebrew window to the /Applications window.
Now, let's make Alfred include macOS aliases in search results:
Open Alfred's preferences, navigate to General > Default Results, and under Extras: click Advanced. A popup window will open that allows you to add file types that will be shown in search results.
Drag the Emacs.app alias from the Finder /Applications window to the popup window. The new entry should read com.apple.alias-file | alias
Close the popup and try searching for emacs. The result list should include the Emacs.app alias.
