Talking to external programs is outside of the scope of libgit2, so it won't talk to git's credential helper. It's considered to be the tool writer's responsibility to retrieve the credentials from the user, wherever they may be.
The credential store is a helper for the git command-line tool to integrate with whatever credcential storage you have on your environment while keeping the logic outside of the main tool, which needs to run in many different places. It is not something that's core to a repository, but a helper for the user interface.
When using libgit2, you are the one who is writing the tool which users interact with and thus knows how to best get to the environment-specific storage. What libgit2 wants to know is what exactly it should answer to the authentication challenge, as any kind of guessing on its part is going to make everyone's life's harder.
Since the Windows credential storage is accessed through an API, it's not out of the question to support some convenience functions to transform from that credential storage into what libgit2's callback wants, but it's not something where libgit2 can easily take the initiative.