There has been a lot of chatter lately on this. Nadal will 95% get a penalty for this withdrawal, but about 80% of the penalties ever given have been lifted after 1 or 2 weeks (Haas' after 6 months) due to a player appeal. This is one of the worst rules ATP have deemed worthy to be in the rulebook so it's impossible to anticipate with 100% accuracy if the year end rankings will feature Nadal with a penalty or not.