It's a stumper for me too; if there is a single trust, it should use a single TIN.
My guess is that when they merged "his" and "her" funds into the trust's ownership, they still kept their funds physically separate from one another. (There should be a 4 hour college course on the variations in how married couples handle their finances.) Reporting the trust's income on two different SSN's would have no effect on their joint income tax return. It's analogous to their having two joint accounts at your bank, one with her SSN and another with his, but it just doesn't quite feel right.
For the purposes of the CTR, I would list both H & W as conducting the transactions and list the trust twice, once with one SSN & account number and once with the other pair.
Yes, I made that up. If you call the Helpline they may make up a different answer for you.