One more more follow up on this as I have a little more information. So I noticed that two nodes seem to have references to the deleted indexes in their data dirs:
es/data-es3/sv/nodes/1/indices/xyz-2016-08-26/ --> Was deleted using the DELETE api
es/data-es3/sv/nodes/1/indices/abc-2016-05-12/ ---> Was deleted using curator (remove,close,delete)
Overall I'm seeing traces of indexes that I deleted in the data dirs regardless of deletion method (curator vs. delete). That being said, I want to avoid the issue of dangling indexes/ unassigned shards in the future if/when I need to reboot these nodes. I know we don't care about these indexes anymore. Is it safe to delete the corresponding data directories to remove traces of these indices? Can I do this while the cluster is running? Any advice is greatly appreciated!