Yep, we had this a LOT, and you're pretty much stuck. DS has a list you can customise (within the settings for each agent, on each computer) that is meant to remove virtual network adapters (from VirtualPC, VMWare, etc), but misses some like VirtualBox, Himachi, etc. It also shows any dual-NIC systems, Bluetooth adapters, Firewire adapters, and more. Controlling what it reports is a nightmare. The only real option is to remove "MAC" from the primary key, but that causes BCD errors when imaging computers using WinPE.
What you could try, although still not ideal, is running Serial Number and UUID. That combination will get around most of the issues with the BCD errors (you'll stillg et some you'll need to play with), but it does appear to fix the duplicates. You will need to manually delete the inactive duplicate though.