It's advisable to update the handle server distributed with DSpace (version 6.2 as of DSpace 3.0) to version 7.2 in order to get IPv6 support.
"CNRI is pleased to announce the release of version 7.2 of the Handle System software. The software is available for download at http://www.handle.net.
Version 7.2 introduces IPv6 capability for handle servers. Although the Handle System protocol has always allowed IPv6 addresses for handle servers, a bug in prior versions of the software suite prevented this in practice. If you wish to make your existing handle server available over IPv6, please contact firstname.lastname@example.org."