Hard links allow different directory entries to link to the same file content. TreeSize's full NTFS support utilizes hard links, e.g. to deduplicate files with identical content.
But what actually is a hardlink? What you see in tools like Windows Explorer are basically hard links. They map a path in the file system on your drive and allow access to the corresponding file. Normally, each hard link points to its own section on the disk, but it is also possible that several hard links point to the same section. TreeSize takes advantage of this fact when deduplicating. It points multiple existing files to the same data and frees up the disk space that was previously occupied by individual chunks of data. After deduplication, the paths in Windows Explorer are still as visible as before, but they all point to the same file.
The disk space a file occupies does not change, no matter how many directory entries link to it. For the exact calculation of the occupied space it is vital to count hardlinked files only once - a task at which the Windows Explorer and most other tools fail.
Since the evaluation of every single file takes up additional time, the determination of hard links may be switched on or off in the "Options" dialog.