I just finished setting up my new install of Yosemite, except for my hotkeys. I decided to use homebrew-cask to install a bunch of my apps this time around, which actually installs the apps to /opt/homebrew-cask/Caskroom/ and symlinks them into ~/Applications.
While my hotkeys are successfully switching between apps, "Toggle visibility for apps" doesn't seem to be working. It does work on my other apps that were installed through the App store, just not with those being symlinked.
I've tried with all of the different trigger behaviors and it doesn't seem to help.
I'm using the latest Yosemite and Alfred v2.5 (299).