My understanding is that "N/A" means "Not Applicable" and is therefore excluded from being part of the calculation in either a positive or negative way. This is why the scores are coming out the way you describe. (5 x "N/A", 1 x "No" and 4 x "Yes" = 4/5 = 80%). It isn't the "No" you are trying to exclude, it's the "N/A"s you are trying to include.
I'm not an expert in this, but my only suggestion is to make the questions multiple choice, with "Yes", "No" and "N/A" as the three answers. Don't allow the question to be marked using the built-in "N/A" (so you have basically duplicated the options you have now) and then make both "Yes" and "N/A" score the same. Then your calculation would be 9/10 = 90% as required.
HTH