I'm working with this plugin to publish exams. In order to get mermaid working, I had to follow the instructions specified in Mermaid.js section in README.md.

This works, but will only reload Mermaid, not other JS features (code.copy, for example).

Relevant issue in mkdocs-material: squidfunk/mkdocs-material#5816 (comment)

Since, all JS associated with document content changes are subscribed to document$:

document$.subscribe(function() {
  console.log("Put your code here") // Executes on `DOMContentLoaded` and on instant navigation
})

We can trigger all subscriptions after a decryption:

function theme_run_after_decryption() {
    document$.next(document);
}

I've tested it in my site, and it works, but it might need further testing.