The article says
"We've measured a 16% increase in wheel drag between a disc-braked wheelset and a standard wheelset", Jean-Paul told us. "We performed a direct back to back test of the Zipp 303FC in standard version and disc brake version, for our own competitor comparison purposes. That 16% is a constant offset in the performance curve across the entire cross wind angle range."
I find this pretty surprising. It looks like Zipp's 303 Disc is a different rim from their 303. I would expect most of the loss from the rotor to be made up for by a better rim shape.