Well the answer is yes.
Adding to the security layer that having indexes enforces by using roles and their allowed to search list of indexes, splunk searches also gain from having separate indexes. The main reason is if you are searching an index that has a high number of sourcetypes and your search spreads through a specific time range, then Splunk would have to gzip more slices of data to check whether the data your are asking for is there or not.
If you are searching one index only, then even if you are searching in more than one bucket, at least you know that you are being more precise.
More, you can specify retention policies per index, not per sourcetype, so it eases up your life having them separated.
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