Update NNX docs for deprecated Variable.value access

[sumitdotml]

What does this PR do?

Updates NNX docs and notebook-backed examples that still used deprecated Variable.value access.

Array-backed NNX variables now use variable[...] for reads and assignments. The non-array traced_dim example uses get_value(). I have left the Linen Variable.value examples and unrelated enum usage, such as transform.value, as unchanged.

Fixes: N/A

Testing

git diff --check
uv run pre-commit run jupytext --files ...
uv run pre-commit run --files ...

Checklist

• This PR fixes a minor issue (e.g.: typo or small bug) or improves the docs (you can dismiss the other checks if that's the case).
• This change is discussed in a Github issue/discussion (please add a link).
• The documentation and docstrings adhere to the documentation guidelines.
• This change includes necessary high-coverage tests. (No quality testing = no merge!) -> These are purely docs-related updates, so test files are not included.

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