Right now Hunk is released as a tar.gz file not a package like rpm. How does an upgrade work?
Just untar it over your current installation. See the installation instructions in the documentation.
Any plans to create a RPM?
What effect does this have on search head clustering?
Good question, I don't know. Presumably you can apply the same steps to upgrade a search head cluster with Splunk Enterprise: See "Upgrade a search head cluster" in the Distributed Search manual.
Did you check the docs?
Here is the link in case you can't find it: http://docs.splunk.com/Documentation/Hunk/6.2.5/Hunk/MeetHunk