There's no great harm in having the early Gatwick-Shannon as otherwise the first London-Shannon flight with Aer Lingus wouldn't get business travellers to their destination before lunch time.
I agree that the timing of both the Shannon and Cork flights are a bit unfortunate. With a second flight a day (even if operated by Aer Lingus Regional), they could tap into a valuable connections market.
Although, the way Aer Lingus might look at it is that all they would be doing would be taking passengers off either dircet services from Dublin or services to Heathrow, CDG, Amsterdam etc.