What is a 'yield rate'? Do graduate department seats go unfilled?

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.

Usually universities make more offers than they have space available. Admissions makes an estimate of the yield using historical data. They make enough offers to fill most of their spaces based on that estimate. Then they wait. If yield is too low to fill the spots, they make more offers of admission.

If too many people accept and there are more students than funding, the next year very few offers will be made. Occasionally, admissions will be closed the next year in a small department.