With the help of NTFS hardlinks you can link several directory entries to the same file content. SpaceObServer, for example, offers deduplication via hardlinks.
The amount of server space that a hardlinked file occupies does not change, no matter how many files link to it. The Windows Explorer, along with many other tools, does not calculate the used server space correctly. Since SpaceObServer offers correct values, scan results may differ from those presented by the Windows Explorer.
Evaluating every file takes time and scans will take longer to complete. If you want to save time, you can switch off the NTFS hard link regulations via the SpaceObServer "Configure Scans" dialog.