Since switching from macports, Homebrew has been just awesome, I use it for my personal installation scripts and it is fast and seems reliable. The nice thing is that it installs the so called casks in their own directory and then symlinks them to /Applications However, last month I discovered two problems:

1. When you use the automatic update features of the applications like NordVPN, it not surprisingly this blows aways the symlinks and you suddenly don't get updates. The solution is not to use the automatic updates and to regularly run brew cask upgrade to get the latest. Then you can run brew doctor and see what is not linked, then manually fix it with a brew link _name of cask_ and this should fix things.
2. The second problem is that there is a method called undent which deprecated and then brew crashes on it, there is a fix scheduled, but it is not clear when. This affects older scripts like rstudio which calls it. You can't even brew cask uninstall because the script itself is bad. The solution is a brute force removal of the cask with rm -rf /usr/local/Caskroom/_name of cask_` which is pretty blunt but solves the problem.