Não tenho certeza sobre os números exatos da sua situação, mas os itens a seguir podem ajudar a tranquilizá-lo ( no link acima ):
Like FAT, the NTFS file system has a certain amount of fixed-size overhead and a certain amount of per-file overhead. NTFS also has several advanced features, including recoverability, security, and support for very large volumes. Because of these advanced features, the NTFS metadata overhead is somewhat larger than the FAT metadata overhead. On the other hand, because NTFS cluster overhead is smaller than FAT cluster overhead, it is often possible to store at least as much on an NTFS volume as on a FAT volume, even without using NTFS file compression.
O NTFS tem a seguinte sobrecarga mencionada pela Microsoft :
It is not recommended to use NTFS on a volume that is smaller than approximately 400 MB, because of the amount of space overhead involved in NTFS. This space overhead is in the form of NTFS system files that typically use at least 4 MB of drive space on a 100 MB partition.
Para Fat32, isso depende do tamanho do bloco e do tamanho da partição :
Blocksize Overhead on 2GB parition (in MB)
512 25**
1024 24**
2048 35**
8192 119
32768 470
(**) You aren't allowed to use these blocksizes for a 2 GB
partition although it probably would be possible.
The table gives you an estimate on the amount of overhead in MB for each of the filesystems described above, when they need to store 30000 files varying in size from 4 to 1000 kB (there are more small files than large files). This includes the overhead for the bitmap or FAT, the overhead for administration blocks and the overhead caused by having to round the size of files up to the nearest multiple of the blocksize. The size of the partition used is almost 2 GB.
Keep in mind that these are calculated figures, and that they represent an average case ... Also keep in mind that a lot of things have been simplified, but these figures should still be accurate to within a couple of megabytes.