A lot of people think Apple is replacing samba with their own version because of the GPLv3 and patents. I’m not so sure that is the case and I think this comment is more on the mark
The reason is that binaries in /System are signed with Apple’s keys, which the haven’t made public. As far as I know this is also disallowed by GPLv3.
Of course it might also be that Apple isn’t satisfied with the progress of samba.