According to the book you linked to, the answer is that it's not ambiguous.
Do you want a cup of coffee?
That sentence asks a simple question, and will elicit the answer "Yes" or "No", depending on whether the person asked wants one or not. The sentence is not semantically ambiguous.
The book you cite, Foundations of Computational Linguistics, says
A pragmatic ambiguity consists in alternative uses of one meaning relative to a given context ... a pragmatic ambiguity by its very nature cannot be disambiguated by the context.
There is no information in your question about the context of the question, but it seems to me that it should be quite clear from the circumstances of the question whether the speaker is offering to make a coffee or not. Because the question can be disambiguated by the context, it is not pragmatically ambiguous either.
The book itself gives an example of a pragmatically ambiguous utterance: telling someone to "Put the book on the table" when there is a choice of two identical tables. If the correct table cannot be determined from the context, the instruction is pragmatically ambiguous.