"Will there be a 64-bit version of the DLC protocol included in Host Integration Server?"

Simple answer - "No".

There is currently no 64-bit version of the Microsoft DLC network stack and one will not be developed for the forthcoming Host Integration Server 2009 product.

You should instead be looking at using IP-DLC as IBM has been moving away from DLC in its products in favour of using Enterprise Extender. Microsoft's IP-DLC link service integrates with IBM’s Enterprise Extender so that you can remove DLC from your network and communicate with traditional SNA applications over the IP network. Enterprise Extender is part of the base operating system, fairly simple to implement and allows simplifying networks to just use TCP/IP. 

Should this path not be an option, then install the 32-bit versions of Windows Server and HIS 2006 (or HIS 2009, depending when you read this blog post) to get access to the DLC protocol.

If you already have 64-bit hardware and are worried about your investment then use Microsoft Virtual Server 2005 to host the 32-bit virtual machine.

[[Thanks to Stephen Jackson, Valerie Thomas, Charles Ezzell for the words]]