The subject disclosure is directed towards a data deduplication technology in which a hash index service's index and/or indexing operations are adaptable to balance deduplication performance savings, throughput and resource consumption. The indexing service may employ hierarchical chunking using different levels of granularity corresponding to chunk size, a sampled compact index table that contains compact signatures for less than all of the hash index's (or subspace's) hash values, and/or selective subspace indexing based on similarity of a subspace's data to another subspace's data and/or to incoming data chunks.