As Scott himself has explained, the bigger deal isn't whether or not it's easy to find out his last name if you know the blog. It is finding the blog from his last name. In other words, if his patients, who don't know the blog exists, find it simply by googling the name of their doctor.
Seems like that would happen eventually whether or not NYT did anything, if SSC got famous enough. Though, I wouldn't dare to tell him how important the timeline of that is. It is his life, after all.
