First, exclude the n/a ("does not apply") from the found set when you do your find to print the report.
To me, it seems like that should be enough, since if you aren't going to show the response, I wouldn't think you wanted to include it in the count of total responses. It seems, though, that you want to see:
Total Responses 18
Which is weird to me. It seems like the sort of thing that would make me distrust the report. But okay.
Create a self-relationship from responses to responses where a constant "does not apply" equals the response, and all other parameters of your search (date range? survey?) are also the same.
For a modified "total responses to this question" field, create a calculated (rather than summary) field. Your calculation should use getsummary and then add the count of the relevant n/a's via the above relationship, which will be evaluated from the first or last record in the group, depending on where you put your subsummaries.
I agree that excluding those responses seems a bit odd. But...
How about an ESQL call that calculates what you want? I have seen a number of recommendations to NOT use ESQL in the schema side of things (i.e. field calculations), but I think that it might be appropriate here. Just be SURE that you commit all records before going to this layout/report (uncommitted records can cause your ESQL to take a long time).
With THAT out of the way, I could see a possible statement being:
SELECT COUNT( answers ) FROM responses WHERE questionID = ### and questionResponse <> "not applicable"
I imagine there are some mistakes in that statemen, so do some testing.