GUI applications installed with homebrew cannot be launched using Spotlight
There are many workarounds for this, 


you can copy Emacs and MacVim direclty to your /Applications folder : cp -r /usr/local/opt/emacs/Emacs.app /Applications/ and cp -r /usr/local/opt/macvim/MacVim.app /Applications/.
You can run sudo chflags nohidden /usr, /usr folder is flagged as hidden but not /opt, this command will unhide /usr so that Spotlight could index it (Spotlight doesn't index hidden directories).
You can also make a shell script and appify it

#!/bin/bash
open /usr/local/opt/emacs/Emacs.app

There is also an option in homebrew , I've not tested it personnaly, that fixes this issue : brew linkapps --system, you can remove --system if you want brew to link your.app to ~/Applications instead of /Applications