I'm betting someone pushed a secret key somewhere and they made the repo private to try to limit the damage...
And if you leak credentials, you'd just have to rotate them. Taking the repo offline would probably be too late anyway and causes a major mess, so not something I could recommend for popular repos
[I work for Elastic]
Since we don't maintain private forks for the Elasticsearch repository (maybe for someone's short lived feature development), the problem of private or deleted forks shouldn't be an issue here.