I was wondering if there is a rule of thumb for the following.
What percentage of students that are accepted for a PhD position were initially put on a waiting list, and were only admitted after high-scoring applicants did not enroll?
This will depend upon the department, but I would expect that relatively few students would be admitted via a waitlist. Departments usually have a pretty good estimate of how many students who they accept will take their offer and enroll in their program.
We don't have a wait list, and actually make more offers than slots, because of the historical hit rate that we have with admissions. Some years, this comes back to bite us, but it all averages out.
A practical matter with waitlists is that you have to wait till Apr 15 before moving to the wait listed students. But by then, they've often accepted a position elsewhere.