[rwmj]

The Windows registry is not a "simple key/value store" by a long shot. It is hierarchical, there are many different types of value, and there's a complex system of security attributes. These are simple facts.

You're right that a file per value would take a whole block on disk given the way some filesystems are currently implemented, but that's not an immutable feature of all filesystems - some Unix filesystems store small files in the inode. A real database is possible, but also the registry must be available very early in Windows boot (actually it's used by the bootloader, but also by the critical device database) so you'd want something that's at least easy to read with a smallish amount of code.