I'm not sure what kind of nutrition certification you are talking about, but specializing in counseling is a great idea. I know of a counseling student who double-majored in nutrition and psychology in undergrad before getting her Masters in counseling because she wanted to specialize in eating disorders. I also know that there is an entire field of "health counselors" where they use counseling techniques such as Motivational Interviewing to help people lose weight.
I definitely second Joseph Young's answer as well--be careful of overburdening yourself with schooling. Making a niche does not always require being enrolled in a whole other program. Find a professional doing what you want to do and ask them how they got there before you make any commitments. In some cases, you just need the experience rather than any official certifications, and you can get that through internships, volunteering, or other means.