It's loaded into the kernel, but it's a kext (kernel extension) rather than being part of the xnu source tree itself. Only a subset of kexts are open source. (By comparison, HFS used to be in the xnu tree, but it was moved into a kext as well a few years back; that one is open source.)

Kind of talking out of my ass, but Darwin can act as a mirokernel, so APFS could be implemented as a user mode service (no idea if it's the case, though).