In prior versions of Elasticsearch, the path.data directory included a folder for the cluster name, so that data was in a folder such as $DATA_DIR/$CLUSTER_NAME/nodes/$nodeOrdinal. In 5.0 the cluster name as a directory is deprecated. Data will now be stored in $DATA_DIR/nodes/$nodeOrdinal if there is no existing data. Upon startup, Elasticsearch will check to see if the cluster folder exists and has data, and will read from it if necessary. In Elasticsearch 6.0 this backwards-compatible behavior will be removed.
If you are using a multi-cluster setup with both instances of Elasticsearch pointing to the same data path, you will need to add the cluster name to the data path so that different clusters do not overwrite data.
Prior to 5.0, nodes that were marked with both node.data: false and node.master: false (or the now removed node.client: true) didn’t write any files or folder to disk. 5.x added persistent node ids, requiring nodes to store that information. As such, all node types will write a small state file to their data folders.