Solution #1
Make your answer options have a value of the score in question instead of 'Y', 'N', 'N/A'.
You can still have the display text of each option be 'Yes', 'No', 'N/A' so that the app user know what to choose.
e.g. your Yes option would have answer value of 3 and display text of 'Yes'.
This is the simplest approach since then all you need to do for a totalling formula is:
{{q1}} + {{q2}} + {{q3}} + {{q4}}
Solution #2
Use the if() function in a nested fashion to check the value of each answer and assign the relevant score based on a true/false result.
if({{q1}} = 'Y', 3, if({{q1}} = 'N', 1, 0)) +
if({{q2}} = 'Y', 3, if({{q2}} = 'N', 1, 0)) +
if({{q3}} = 'Y', 3, if({{q3}} = 'N', 1, 0)) +
if({{q4}} = 'Y', 3, if({{q4}} = 'N', 1, 0))
Solution #3
Add a hidden field for each question, with the hidden field containing just the if()formula for its associated question.
e.g. Hidden field named q1Score would have a Dynamic Value formula of:
if({{q1}} = 'Y', 3, if({{q1}} = 'N', 1, 0))