Murray will probably get a zeropointer, not because he's a committed player (he has played 4 ATP500 tournaments in the calendar year as Monte-Carlo is included), but because he didn't go on-site to Basel to have his back injury checked and probably doesn't intend to go on-site to make some promotion. Finally except if he announces that he will miss Bercy and the WTF, he will not miss the Tour for one month because of his alledged injury.
Nishikori's case is also doubtful but it seems that he made some efforts in this case, and considering my experience, I think he will manage to avoid the zeropointer as the ATP seems to be generally very "understanding" with the rules.
Murray's case looks different and careless : it seems that he didn't even announce his withdrawal directly to the organizers as the Basel tournament website news say that the news came from the ATP staff's site in Monaco. And Murray probably doesn't care about the 90 points he will lose : he had already been careless about such points in the past, as Isner also has been sometimes.
As for Baghdatis, he withdrew to attend his child's birth, I guess the ATP will be human enough to consider that as a good reason.
Nadal, Djokovic, Fish, Monfils, Chela and Roddick will also get a zeropointer but for another reason : because they will not respect the commitment to play 4 ATP500 tournaments in the calendar year.
Stepanek's case is the strangest of all : I had never seen such a case before. He's a committed player and having not planned to play in Basel, he was going to get a zeropointer for not playing 4 ATP500 tournaments in the calendar year. Then he asked to play qualies. But then, he could have avoided playing qualies by taking the additional wild-card which is kept for committed players in every ATP500 tournament as Djokovic didn't ask for it (and I can't imagine Basel staff refusing and preferring taking Garcia-Lopez as an alternate rather than Stepanek as a wild-card). But no he will keep on playing the qualies. I will like to see what the ATP will do in such a case, esp. if Stepanek doesn't qualify. Well, temporarily, I will rather guess that he will not get a zeropointer as he clearly made an effort and maybe talked with the ATP staff about the consequences on his ATP points of playing the qualies.
I will never understand what's supposed to be fun in this youngsters' world, my words were harsh but realistic (or maybe being harsh is enough to be funny