From the PDF:
"On the long term we believe that post-install scripts are a problem by themselves (they still need an install step, and can lead to security issues), and we would suggest relying less on this feature in the future, possibly even deprecating it in the long term. While native modules have their usefulness, WebAssembly is becoming a more and more serious candidate for a portable bytecode as the months pass."
WebAssembly is not "more and more a serious candidate" to replace native modules.
The issue with post-install scripts needs a better long-term solution, but simply deprecating native modules is not it.