If you’ve turned on the “Use macOS LaunchServices database” option in the Options pane of your Applications indexing rule (which is the default), application aliases will not be indexed, because they are not registered in the LaunchServices database. The database only provides a list of all installed applications at their original locations.
If you turn off this option, the actual contents of your hard disk will be examined, and application aliases can so be considered as well. However, indexing may then take somewhat longer compared to using the database (depending on the number of files and subfolders within the indexed application folders).