That's expected, and by design.
Virtual disks in ESXi consist of two files, a small header/descriptor .vmdk file, which contains metadata about the data file's disk name, size, geometry, etc., and the flat (in case of snapshots delta, or sesparse) .vmdk file, which contain user data.
It's the small descriptor .vmdk file, which is used in configuration (.vmx) files, and most commands that are available from the CLI.
André