Sorta. All data being indexed, no matter which Index it goes into is being counted toward your license. EXCEPT data you put into summary indexes, and also all events going into the internal indexes are NOT counted towards your license.(Kristian Kolb)
If you are indexing the same data twice. I.e. if the same data is going to Index1 and Index2, then ALL data is counted against your license. So in that sense your data is counted twice.
see this doc - 1http://docs.splunk.com/Documentation/Splunk/4.3/Admin/HowSplunklicensingworks
Specifically, “Splunk licenses specify how much data you can index per calendar day…”
I'd recommend you download and install the Deployment Monitor App. This will really help you get an idea of what data you are indexing, and from where, and how it is being counted against your license.
... View more