Datastore runs on top of Megastore [1]. You can find out more about our data model here [2], but it's definitely not limited to key-value data.
Our end users don't have to think much about our storage system, though, if we're doing our jobs right. :)
[1] https://cloud.google.com/datastore/docs/articles/balancing-s... [2] https://cloud.google.com/datastore/docs/concepts/entities