Note that headlines are almost never written by the authors of articles, whether in a publication like this or the New York Times. (Something to remember before reacting to a headline.) The headlines are written by someone at the publication who's often less well-informed than the author, or has a different opinion, or is maximizing for eyeballs (clickbait), etc.
In this case, the article consistently uses “[medical] manikin” for its topic, and only once uses “These are not the department-store mannequins familiar to most of us today” to distinguish this from a different topic. It is only in the headline (and thus you know it to be introduced by the headline writer) that you'll find the variant spelling “mannikin” (which outside of this article is more often used for a kind of bird).
Because mannequins almost exclusively refers to showroom figures. Manikins usually is the diminutive for man/people and usually refers to medical models of people though also small sculptures of people.
