A Finder alias (not a symlink) will be added to spotlight, if it's sitting in a visible folder, like Applications.
You can create them programmatically using AppleScript (use osascript to integrate with other shell scripts.)
To create an alias use make alias file to {file to alias} at {destination of alias}.
By default (ie. if destination isn't specified) the alias is created on the current user's Desktop, ie. ~/Desktop.
Here's an example script to create an alias of a file in /Applications
set target_app to POSIX file "/usr/path/to/app"
set alias_dest to POSIX file "/Applications"
tell application "Finder"
make alias file to target_app at alias_dest
end tell
By the way, osascript accepts input from stdin, so to run an AppleScript in a shell script, using a heredoc will work. It may make it easier for you to setup the target file better:
#!/bin/bash
TARGET=/usr/path/to/app
osascript <<EOS
set target_app to POSIX file "$TARGET"
set alias_dest to POSIX file "/Applications"
tell application "Finder"
make alias file to target_app at alias_dest
end tell
EOS