I really enjoyed this article and it's got some great tips in it. I've seen countless examples of shell scripts being treated as second-class code citizens and given how important they are it's so unhelpful to do that.
I totally agree that they should be version controlled - as all code should - but I think encouraging a 'shell-scripts' repo doesn't help to elevate them up to the level of tools written in other languages. For example, I wouldn't have a 'python-scripts' repo or 'java-apps' repo - I don't care what language a tool is written in, I want to know what it does.
StackExchange/blackbox is all shell but it's barely mentioned on the project page - it's a tool and you shouldn't need to know how it's implemented to be able to use it.