I strongly suspect it will work perfectly. Have not ran it through a test cycle yet. However, the reason that's not been done is because vNext is not too far away, and that one will definitely work with 6 (which is a hard requirement for us of course). Be sure to hit the "subscribe" button on http://apps.splunk.com/app/1293/ so that you are notified when the new app ships.
In the meantime, you could spin up a copy of Splunk 6 on your workstation, setup your existing v5 index server as a search peer, then install the v1 NetApp app on your new Splunk instance and see what happens. Should be a pretty short exercise.
Note that you will not need to actually configure the data gathering on your workstation, so disable any scripted inputs / file monitors. The act of performing a search e.g. "index=netapp" will ask all search peers, and get the data that way.
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