Yes. Those employees can still receive something through their own employer rather than nothing, and documenting a spouse waiver makes the enrolment picture reflect what is actually happening.
What a carrier makes of that depends on the carrier and your group. The job on the first call is to get eligibility and waivers right, not to pretend the headline enrolment number is the whole story.
It may look worse on paper than it is in life. Finding out who is actually covered elsewhere, and writing it down, is where the review starts.