De um artigo da MS intitulado Otimizando o NTFS :
All NT disk file systems, including NTFS, use the cluster as their basic unit of storage. Regardless of how small a file is, it must take up at least one cluster of disk space. Thus, very small files that are smaller than a cluster waste disk space. (Files that are less than 1KB are an exception. The system stores these files within the MFT File Record Segment—FRS—that refers to them, instead of storing them externally.) In addition, when a file doesn't end on an even cluster boundary, the file's spillover takes up another full cluster, wasting space. The larger the cluster that the file spilled over to, the more space is wasted.
A parte em itálico informa por que arquivos vazios são relatados como ocupando nenhum espaço em disco (o espaço ocupado pela entrada da tabela de arquivos não é incluído nos cálculos).
Editar: outro artigo útil detalhando o processo exato seguido.