I doubt if they counted them as passengers at all.
Maybe you're right. It's just that 9,000 extra passenger movements would certainly be material to Shannon, particularly when it's the difference between having to admit to a slight fall in passengers, as against being able to shade over 1.4 million. That would be worth a cost of a few tens of thousands of euro, just for the spin. Ryanair might have cut a good deal for them, too, seeing as how it would help the softer image they want to cultivate.
I mean, Shannon would see, what, an average of 3,900 passengers a day? So this would be like getting another two days of passengers.
It would be great if some journo actually put the question to them. I'd say the reply would be comical.