This is by design, following IRS instructions. The relevant information can be found on page 10 of the Form 990 instructions or page 22 of the Form 990-EZ instructions:
The paid preparer must enter the preparer’s identifying number and the firm’s EIN only if filing Form 990 for a section 4947(a)(1) nonexempt charitable trust, not filing Form 1041, U.S. Income Tax Return for Estates and Trusts. The preparer’s identifying number is the preparer’s taxpayer identification number (PTIN), if obtained, or the preparer’s social security number (SSN).
This information applies to all years of the UltimateTax software.