NTFS supports compressed folders - if your drive uses them and if the files in those folders are easily compressible then it's quite possible you could fit 2TB of logical data on a 500GB drive.
Compressed folders are usually shown in a different colour. This is controlled by the folder options dialogue box - select the "View" tab and scroll to near the end of the list to make sure that the "Show encrypted or compressed NTFS files in color" option is checked.
NTFS also supports "sparse" files - these are files that have unused space in them which is not actually allocated until its needed. For example a database could potentially be preallocated to a certain size, yet have thousands of uninitialized rows of data which wouldn't take up any actual space on the disk until they were written to. I'm not sure if a sparse file can have an allocated space larger than the disk itself, but if it can then this could be another explanation.
On the system drive in WHS, there is a D:\Shares folder and a D:\DE\Shares folder.
For all the other drives, there is only the D:\DE\Shares folder.
I was getting confused and jumping straight to the first "shares" folder I saw (in the root directory). This has tombstones to all files that was on that system and hence, no data there, but apparently still lists the size of the original entire WHS system (and hence the 2+ TB of data).