This is especially frustrating when several cookbooks modified and there are no indicators of what's already committed, what files were touched added, removed or modified in the end.
So, I've modified 'tree-view' component - one of core components Atom has, which is responsible for showing directory view on the left, so that now it shows statuses of all nested repositories (no matter how deep nesting is) giving good overview on the changes being made.
Here is example how it looks:

Unfortunately Atom maintainers in the end closed suggested Pull Request -
https://github.com/atom/tree-view/pull/469
Reasoning is unclear and vague.
However, I've made release of tree-view from own fork.
Notes:
Works quite well even with >200 nested .git repos, though with some minor limitations:
- If there are a lot of nested. git repos then start-up time might noticeably increase(with ~200 repos it was 10 sec). The reason is that GitRepository object seems to be not fully async while refreshing status.
- Status refresh of GitRepositry objects on window_focus event is disabled, so if repos changed out of the Atom it might reflect wrong status. But there is option (right-click or assign shortcut) to force-refresh status of a subtree (recursively) or specific repo.

or via command palette.
Download tree-view:
https://github.com/jarig/tree-view/releases/download/0.228.0-jarig/tree-view.zip
Installation instructions:
- Unpack contents to ~\.atom\packages\tree-view
(on windows C:\Users\[username]\.atom\packages\tree-view) - Re-open Atom
Verified to be working with Atom version 1.42.0




