You are still required to report your travel details to INIS if you intend to travel for more than 6 weeks per annum after your application. It is explicitly pointed out on the
citizenship webpage.
If you are outside the State for longer than 6 weeks after you submit your application, you must notify ISD by letter or email to explain why.
Strictly speaking, 90 days mean 90 days. Not 1 day more. However, in reality, the Irish immigration unit is very lenient compared to most other countries. Border officers don't ask that many questions. COVID-19 is another factor that may cause people to be stuck abroad. Many people were able to get in without any questions asked. They won't be able to get your absence days at the border instantly.
It also depends on your nationality. As an EU national who has lived in Ireland for 5 years, you automatically obtain permanent residency and you can leave for 4 months or 6 months or 10 months - nobody would give you any hard time (as long as you don't want to apply for citizenship).
As a non-EU who has a residence permission (other than 4EUFAM and IIP), your future renewal *may* be impacted if you leave the state for more than 90 days, although nobody really has any detailed numbers as to how many people were rejected renewal or being refused entry solely based on this.
