When to answer a question with 沒有?
The answer to 你在做飯嗎？is still 是 or 不是 . To answer 有 or 沒有, the question should be 你有做飯嗎？
Example:

You see your friend washing vegetable, and ask 你在做飯嗎？ (are you cooking dinner?) and his answer could be 是 (yes) or 不是 (no)

A wife came home and saw her husband eating pizza, so she asked 你有做飯嗎？(have you cooked dinner?) the answer could be 有 (I have) or 沒有 (I have not)



If the question is 你做飯嗎? (are you cooking (now)?/do you cook (regularly)? ) then you can answer according to the context.
If you mean 'I am not cooking now' then you would say '不是' (no)
If you mean 'I don't cook = 'I haven't been cooking regularly' then you can answer '沒有' (I have not)