Not ticking boxes in recommendation forms
It can definitely hurt the students.  Having worked on master's and doctoral admissions in my own department (physics and astronomy) and occasionally been consulted by faculty in closely related departments (chemisty and applied math) about unusual applicants, I can attest that there are some faculty members that do pay attention to those checkbox rankings.  They are not numerous in my department, but they do exist.

In most cases, the students' test scores, grades, and recommendation letters speak for themselves.  For a strong applicant, those checkboxes are probably never going to cost them an admissions slot.  However, when there are some questions about the strength of a recommender's letter, some people of the committee do turn to the numerical ratings to try to get a clearer idea of the applicant's abilities.  So if you write a student a compelling recommendation letter, those boxes will likely never matter; however, if your letter is short or expresses possible reservations about a student, you may be further hurting the student by leaving the boxes blank.