We've established that modern hard disks and SSDs work with clusters of 4096 bytes. However, they communicate with the rest of your PC as if they still have clusters of 512 bytes, via the LBA (Logical Block Addressing) method. Even the most state of the art SSDs are controlled by the operating system as if they're devices with 512 byte clusters. The reason for this is that it guarantees compatibility, and it's referred to as 512e or 512 emulation.
It means that each physical sector is divided into 8 'logical sectors' that are available to the OS.
Modern file systems work with clusters of 4 kilobytes, which means that files are divided into 4 kB clusters. 4 kB is the small storage amount (which means that a file of a couple bytes takes up 4 kB of space) and the physical file size is rounded up to 4 kB. On average, each file that's saved is 2 kB larger than in reality (which you can see when you open File Properties, see image 2), but it also means that it's easier for the OS to use the disks. Losing a few MB really isn't a big deal considering how large disks and SSDs have become.
In the near future we expect to see ‘4k native’ disks that will also communicate in sectors of 4096 bytes. Windows 8 and Windows Server 2012 are the first Microsoft operating systems that support these 4k native disks.
Almost all modern file systems, including NTFS used by Windows, work with 4 kB clusters. That means that all files take up an average of 2 kB of extra space.