Win32 APIs like CreateProcess suck because they have to spend so much time setting up the stuff that allows Win32's application model to mimic that of 16-bit Windows, which was coopreratively multitasked. The NT kernel is much faster at creating processes when it doesn't need to worry about that stuff.

As for NTFS: it's not NTFS specifically, it's the way the I/O system is designed in the NT kernel. Imagine any call from outside that layer transitioning through a stack of filter drivers before actually reaching the implementation. Very powerful stuff, but also very bad for performance.