[jvert]

Raymond is almost always 100% right, but in this case he (or Adrian) is a bit off. The mini filesystems in NTLDR can absolutely traverse subdirectories. After all, things like the kernel are found in places like C:\WINDOWS\SYSTEM32\NTOSKRNL.EXE and NTLDR has to load that. There is a "nanofilesystem" in the boot sector(s) which only knows how to load C:\NTLDR, but NTLDR could easily restore a hibernation file that was in a subdirectory.

The real reason these are in the root is because There Can Be Only One. You can have multiple versions of windows in different directories on the same drive, but only one NTLDR or BOOT.INI or HIBERFIL.SYS. If you put them in subdirectories, then you can now have more than one and NTLDR doesn't know which one to use.

And as somebody else pointed out, this all got rewritten after Windows XP.