What is a 'yield rate'? Do graduate department seats go unfilled? This link states that the university has a yield rate (acceptance rate) of 40%. Does that mean 60% of seats are not filled at the end of cycle? 

Or does it mean university makes more offers than seats present and 40% corresponds to seats the university has?
I had a look at the link you shared. The yield rate is defined as the number of applicants who accepted offers of admission divided by the number of offers of admission. Yes, it is indeed true that graduate departments send out more offers of admission than "available seats" and forecast a number of enrollees that is approximately the capacity of the program.

This creates some challenges when admitted students receive offers of graduate financial aid like teaching assistantships, research assistantships, or fellowships. But it is the job of the graduate programs director in any particular department to develop an admissions strategy that meets program goals while remaining financially feasible. For this reason, you often see active waiting lists for graduate programs admission.