I have a simple question, Does using indexer clustering affect Index Per Day license usage? for example, if I have a 100 GB/Day license and use 3 indexers with the replicate factor of 3, my license will be used 3 times or not?
Indexer clustering and replication have no effect on your license.
Storage is another matter, of course. The higher your replication factor, the more storage you will use.
How about a link to a document? https://docs.splunk.com/Documentation/Splunk/8.0.3/Admin/Distdeploylicenses#Clustered_deployments_an...
"Only incoming data counts against the license; replicated data does not."