> When you reorganize files, now references need to be updated in many places.

This is exactly why directory based namespaces are a good idea.

Otherwise:

1. You refactor. But namespaces which were formerly in sync with dir structure, but now aren't because you decided to move directories around to manage code better.

2. You don't refactor because it's a lot of work.

> I hate it in TS/JS

It's not only JS/TS. Python, Go, Rust ....

C#'s approach here is redundant, and due to copying whatever Java was doing.