Hi Jenny and Happy New Year!
There should be hotels in Dublin with a 24h check-in policy for such scenarios. I would look at the 24h front desk hotels you mentioned and then contact the ones that interest you to know if they also offer late check-in.
Please know that you can still get into the city centre from the ferry port by
public transport up until 12:30 am or by using a cab.
Do you already have plans during your time in Dublin?
Cheers,
Antoine