I was just looking into their program today. I have a ton of respect for NACADA and since they have written the standards their program should be legit IMO.
As far as the certificate program you would have to sign up for the Masters program and then only take the classes tha apply for the degree. It's kind of dishonest though because you couldn't tell your advisor that is what you are doing since I don't think that they would be allowed to let you proceed ethically speaking.
That being said... none of the courses have a pre-req so it shouldn't be a problem. Unless they have academic policy that specifically states that you cannot earn a Certificate if you are in a Masters program that you haven't completed.