I've wondered this as well, i recall an interview with someone from cityjet (ceo possibly) saying they were concerned they may lose their fifth freedom rights to operate to the continent from LCY, and that they would only be allowed to operate to the UK from Ireland. An exaggeration maybe, but it does raise the question.
The UK and Ireland have always had their own deals outside of the EU though, so maybe a UK company will be allowed to own an airline with an Irish AOC and vice versa?