Is it possible to configure NetWare Core Protocol to run over IPv6?
NCP is a generalized communications protocol, and it currently rides primarily upon IP -- IPX has long been deprecated even by Novell. As such, it does indeed support IPv6. The primary platform for NCP is no longer Netware but Netware's successor product Open Enterprise Server (OES) which provides proprietary Novell services (such as NCP) as an add-on product to SuSE Linux Enterprise Server.
There is documentation for using IPv6 with Netware (confusingly labeled as OES in Netware's last iteration) at http://www.novell.com/documentation/oes/pdfdoc/ipv6/ipv6.pdf
Documentation for IPv6 on OES 2 and 11 would start with the documentation for dealing with IPv6 on SuSE Linux versions 10.4 and 11.1.