Just downloaded https://squeak.org/ to play around with this concept.

I wonder if there is already a modern tool/suite for Node/Python inspired by Smalltalk...

Consider playing with Pharo [1], it shows how it can still use Git to store sources in background.

There is LivelyKernel [2] but some versions are more file-oriented (like Lively 4 [3])

[1] https://pharo.org/

[2] https://lively-kernel.org/

[3] https://lively-kernel.org/lively4/lively4-jens/start.html

Very nice. Squeak is also my first choice for Smalltalk environments. I'm not much of a Smalltalker but I know several who were real involved.