Sorry for the slow reply, I've been offline.
A notified body should not require a draft or non-harmonized standard to be used, in practice their best shot is to say that the non-harmonised documents should be viewed as an input to your risk management process, which allow for action in the case that significant risks exist which is not worth waiting for the harmonisation process to be completed. This argument is valid because EN ISO 14971 is a harmonized standard, and it in turn it is reasonable that draft/non-harmonized standard provide material for identifying hazards, and also may establish state of the art.
As for phthalates labeling, I'm not an expert, but I was assuming that we are not talking about any significant risks. Thus, waiting for at least the publication of the standard seems reasonable. There may be special cases where immediate action could be warranted, but in this case waiting for March 21, 2010 is equally not justified.
You may ask what to do since the essential requirement is so specific (labelling is required). Well, it's a long story but basically there is no legal requirement to answer essential requirements directly, as long as all harmonized standards are applied. If you look closely the MDD is a bit of a mess for this point (there is some history here going back to 1984, far too long to explain here). But the upshot is, in my professional opinion, where there is no harmonized standard for an essential requirement, only EN ISO 14971 must be applied. So, see the two paragraphs above.