Anyone using it with nodejs to make a sandbox for code agents?
Yes. More than a few times. It however is not really designed to operate as a secure sandbox environment.
https://nvd.nist.gov/vuln/detail/CVE-2025-68668
ChatGPT's Canvas uses Pyodide for sandboxing, but it's not designed for coding agents. Node.js environment is usually better for agents. Pyodide restricts server-side functionality, and fetching external URLs often needs proxying due to sandbox. By the way, pyodide is still good option for interactive visualizer or deploying small webapps require data processing.
For that purpose I think most people are using bubblewrap or seatbelt/sandbox-exec with CPython.
I've done some experiments along those lines with Pyodide in Deno: https://til.simonwillison.net/deno/pyodide-sandbox