I have never heard of any rule on this.
IMHO, if we are referring to the pontiff in a formal way, we would speak of a new document officially promulgated by Pope Benedict XVI. In more relaxed discussion (such as on this board) it’s perfectly fine to skip the number, unless there is confusion.
In the mass, even though the text is rather formal, the reference seems more personal because the title is left for after the name. We are praying for Benedict, who happens to be the 16th, and happens to be pope. The reason we are praying for him is because he occupies that office, but my take is that we are not so much praying for the office and officer as we are praying for the man who occupies the office. So I would skip the number.
I may be reading way too much into this, so I will be interested in hearing about the history of this custom, and how it is done in other languages, which should inform our use in English.