Agent Lass states that the Chesapeake Ripper took from a victim, among other things, the thymus. The thymus is a gland that is part of the immune system, and atrophies from birth. By adulthood, it's little more than a nondescript fat nodule just above the heart. There would be no point in taking it, and even identifying it would be tricky.
The crime scene visited in flashback has two police evidence cards for both numbers 3 and 9. They're supposed to be unique.