If my tutor on a QS9000/TS16949 transistion course is to be believed, then the '16' refers to the number of amendments( however big or small) there were between 9000 and TS and the '949' equates to the number of companies initially involved/ affected by the new standard globally.
Don't know if this is the real reason, and can't qualify it, as my company is still struggling with the 9k2k transition, but if he's giving courses out on the stuff, then it could be true !
Paul.