It's actually the opposite; an increasingly large proportion of the passengers on those flights have TSA Global Entry preclearance, for whom the Shannon stop-over is a nuisance.
Global Entry was rolled-out to UK citizens in November 2015. It is very, very quick at the destination: scan passport and a couple of fingers at a machine and take the 'entry ticket' it issues. Shannon does have Global Entry kiosks but those travellers don't save any time using them there.
Given that, the time-saving of flying from London City is more than eaten by the time on approach and on the ground at Shannon. So why not just fly from Heathrow?