I have set up pooled search heads over clustered indexers for customers on both Splunk 5 and Splunk 6, so those two features must be compatible.
Each search head is added to the cluster under the search head role, and each search head is added to the search head pool as you normally would. The master node doesn't reference search heads at all, regardless of their pooling state. See http://docs.splunk.com/Documentation/Splunk/6.0.3/Indexer/Enablethesearchhead#Add_search_heads_to_a_cluster for reference.
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