Calculating writing system efficiency with respect to reading ambiguity?

The problem is with formulating the task as reading ambiguity. Ambiguity is a function of context not simple homography. Spoken language is full of all sorts of ambiguity some of which is reflected in written language. Orthographies introduce new ambiguities and remove others. For instance, the example of final devoicing given in the other answer. It reduces potential ambiguity with respect to word derivation but introduces potential ambiguity with respect to word shape. But neither of these represent real ambiguities for actual speakers of the language.

What's worse, because the types of ambiguities and the corresponding disambiguation strategies will be different across languages, whatever measures you use for comparison will be highly suspect. How do you compare the impact of the unmarked word stress in Russian with the unmarked vowels in Arabic or the unmarked tone in Pinyin? They all have very specific consequences which cannot be captured by a single number.

You could look at it from the perspective of the learner (native or non-native) but even then, you need a much less precise number. How do you compare the precise transparency of e.g. French, Italian, Spanish and Greek orthographies? We can intuitively say that French and Greek are similar and Italian and Spanish are also similar. But from the perspective of a learner (or any other practical perspective I can think of), the precise ranking of Italian vs. Spanish is irrelevant.