Configuration in Elasticsearch 2

I have 3 elasticsearch nodes (running 1.1.1 version) and the following configuration.

index.number_of_shards: 3
index.number_of_replicas: 2

I am upgrading to Elasticsearch 2.0.
In elasticsearch.yml in 2.0, I did not see any values for default number of shards and replicas. Are these still allowed in 2.0?

Yes, they're still valid. The documentation is the authoritative reference for this.

The elasticsearch.yml that ships with ES doesn't contain all valid configuration parameters.

In an ideal world it should though, so please feel free to raise an issue to get it added (either in the file or in the docs).