IBM does have a tool that properly counts CPUs and cores for value unit licensing calculations. It's called Tivoli License Compliance Manager. Load an(other) agent on all of your TSM systems and periodically it will pop out a report of all your value units. List price about $26/CPU.
I agree that TSM should contain something to help out with licensing, but be careful what you ask for - other vendors that do that enforce licensing by server (you have to get specific license key registrations for each server). Not a good tradeoff. Bill Mansfield Solution Architect Logicalis, Inc.