Imagine trying to explain to someone how math operations work in js, you wouldn't really want to explain how numbers are represented in the computer until you get to something that necessitates that understanding - like bit operations.
So, I'd just say it depends on your goals, if your goal is to explain precisely how every detail of something works, then yes I'd agree with you, there's no excuse for magic. But if you want to explain how a general concept works I'm fine with loads of "magic" holes you can fill in for yourself later.
To describe something as magic in a serious context is toxic. We're not sleight of hand performers, we're engineers. It's more helpful to state something like, "this library is complicated and the internals are beyond the scope of this post". A pointer to documentation and source code on libuv would be even better. In face, this series of articles on libuv are a great start for those who are interested: https://nikhilm.github.io/uvbook/introduction.html
Also the 'magic box'.
The Urban Dictionary (the place where I look for colloquialisms) has this definition: "with or through complexity either spurios to the contemproary context or to long to be reasonable or desired of explanation". [1]
1: http://www.urbandictionary.com/define.php?term=magic&defid=9...
Until, of course, the final chapter (or was it the chapter before the final chapter), where you learned that magic isn't real.
However, there is nothing occult about software development and we shouldn't use "magic" as an excuse for not understanding or describing things thoroughly. Just imagine your doctor explaining you a surgery in these terms.
Otherwise, a very good and refreshing read.