To use the integrated Dedupe, you MUST have a 64bit Windows 2003 or 2008 server.
If you use the appliance dedupe from ExaGrid or Quantum, you can stick with a 32bit OS.
Oh and a 64bit OS is required for Exchange2010 as well, or Exch2007 on 64bit too...
There are minimum requirements for BE that are different than older versions, I suggest you read up on them.