I'm not involved with Hamachi anymore, so I took what they told me privately about IPv6 at face value. I know the work on it started back in '09 and there were some v6-related bugfixes referenced in the release notes.
WRT 100.64.x.x. - back in '07 we pitched IANA an idea to have a dedicated class A network for VPN service providers. This was based on the assumption that while many people might use VPN networking, very few would be on two VPNs at the same time (which is neither too practical nor advisable). So having this space would've meant not needing to compete and resolve conflicts with 1918 addressing and it would also provide single direct-routed space within a VPN that natively supported OS broadcast traffic. Latter is a very big deal in Windows world, because of how a large chunk of Windows Networking works, and it's generally a useful thing to have for proper LAN emulation. IANA just waved us off.
(edit) Followed a link at the post you linked to and there's an official news release that says -
We’ve added IPv6 support to Hamachi a while back, and you can
simply turn off the use of the 5/8 space, but we realize that
IPv4 is still very important to most of you.
It sounds like the IPv6 support is there, but the client defaults to IPv4 addressing. This has probably to do with user-facing issues of using IPv6 (like customizing passthru rules in firewalling software and such) rather than with an inherent inability of Hamachi to run outside of v4 space. It is capable of pure tap tunneling after all.