Don't see how this re-release would have much effect on their value, given that the original games themselves have been "preserved" by many countless times over across the Internet, likely since Doom's launch. Not to say the disks are any less of a collector's item.
I was thinking that as the "new" versions make their way into the market the original versions might be harder to come by. But I agree, it's more about the physical disks with labeling than the content. I wish I still had the boxes.