For example, the exenstion “Always shot workspace thumbnails” added support for gnome 49 a month ago:
but it still using an old version in nixpkgs-unstable?
So does the fact that extensions.json was updated last week mean that all extensions was synced, or is there something else that needs to be done as well?
The upgrade script is run manually when someone remembers to do it and it updates all automatically packaged extensions. And changes to extensions.json are almost always done by the script.
But for a changes to an auto-packaged extension to be picked up, a release must be published on extensions.gnome.org. In your case, it looks like they did not even push a tag to their Git repo.