It's because manufacturers mix up gigabytes (1,000MB = 1GB) and gibibytes (1,024MiB = 1GiB).
The terms kilo, mega, etc mean 1,000, 1,000,000 etc. So a megabyte is equal to 1,000 kilobytes, which is 1,000 bytes.
A gibibyte is 1024 mebibytes, which is 1024 kibibytes and so on.
Your iPod Mini has 6GB of storage, which is less than 6GiB. Obviously, some will be taken up by the iPod software, but not much.