There's a few factors that will have fed into the extra 6K in Cork, beyond the scrapping of Shannon-Heathrow. There was a marginal drop in traffic from all other London airports to Cork. The route was using an A321 instead of an A320, which while probably usually not filled, would have taken extra passengers on Friday, Sunday and Monday services. Also, Cork-Southampton was running in Feb 2007, but not Feb 2008. Some pasengers headed to/from Hampshire/Dorset etc. will have flown to/from Heathrow instead. I'm sure some will have come from the Shannon service, but not all.
Actually, I'd have little doubt the the CityJet service will get good loads. The yield is what needs to be worried about. There was talk of other airlines that have given great press releases only to pull a route later and the example of Malev in Cork is the one to worry about. The loads were always good on Cork-Budapest, but the tickets were all being sold at the lowest price and for an airline that doesn't have the cost structure of Ryanair etc. that's an impossible position to sustain. So the question is how many seats can CityJet sell for E300+.
As for the small regional airports... Don't get me started... Sligo is looking for substantial funding to extend its runway out into Sligo Bay, yet Sligo is only 55km from Knock Airport with its perfectly adequate runway. When you consider Limerick is 25-30km from Shannon and the time spent travelling from Sligo to Knock would be less than a journey from Dun Laoighaire to Dublin Airport, it just doesn't make sense. These places have the ability to become money pits that also undermine the economics of the larger regional airports.