First, for full-time professional employees, certification is similar to lifeguard certification, exercise teacher certification, and pesticide application license for example. If an agency has a precedent of paying for these certifications, it may not want to pay for professionals' certification too. Second, agencies are indirectly paying for part of certification. Again, it's usually the agency. Based on the facts and arguments presented, it appears logical that the employee should be paying for his or her certification.
Agencies contribute to much of the employer's professional betterment.
Certification is where the professional should assume the financial responsibility.