Nadal lost to Del Potro in the semis @ Shanghai and has now done the same against Ferrer right before he was to face Djokovic both times - both in straight sets.
Even though Nadal could have leaned on the fatigue crutch even if he lost to Djokovic in both finals, it STILL would have been worth it for psychological reasons if nothing else for Djokovic.
This season Nadal has defeated Djokovic three straight times and has lost just once @ Beijing final. Shanghai and Paris would have evened the series - on paper.
More importantly, if Djokovic is able to capitalize on the still existing slim chance of ending the year as No. 1, having done so after defeating Nadal would have meant that much more - even with the fatigue BS.
Could it be that Nadal and his camp has engineered the current state to deny Djokovic the satisfaction and psychological cushion - as long as the 'participation' is able to secure the No. 1 rank for Nadal - without collateral damage? It's possible given what's at stake for Nadal next season.
Nadal HAS to win at least two Slams next year to have a realistic shot @ matching / passing No. 17 and with a very strong possibility that the two wins WILL come at the expense of Djokovic in the finals, you cannot discount the maneuvering completely.
Djokovic wins - without beating Nadal - and with the absence of Murray AND Federer while barely scraping past Del Potro in the finals @ one of them does rob him of the juice that legitimizes his claim to return as top dog. Facing and defeating a fatigued Nadal would have covered at least some of that gaping terrain.