Snap, I too am an Irish citizen married to a non-EEA national. Hello!
Being the family member of a qualified person does circumvent the 90/180 rule or similar limitations on the residence of non-EEA nationals, and that's literally one of the basic principles of EU free movement law. That the qualified person can take their family members with them, to live.
It comes from the principle that member states should be facilitating free movement rights. Part of this is the ability of the qualified person to bring family members with them.
Here is the information the Irish government provides for Irish citizens exercising free movement rights. You'll notice there's nothing there about 90/180 day rules or similar applying to their family members: because they don't.
www.citizensinformation.ie/en/government_in_ireland/european_government/european_union/freedom_of_movement_in_the_eu.html
Here is some information from the EU itself, stating that family members have the right to reside and work in another country.
ec.europa.eu/social/main.jsp?catId=463&langId=en
This doesn't mean that any time an EEA national goes to another member state they're exercising free movement rights though. If you're going on holiday for a week, free movement rights aren't really applicable there. Which may explain why your DH wasn't treated as the family member of a qualified person in those circumstances.
That said, DH has been through the EEA nationals gate with me before when entering a member state (Portugal, as it happens) and got a stamp. I think because I could in theory have simply arrived with him, told them I was going to exercise my free movement rights and live there and they'd have had the obligation under EU law to facilitate his residence. They probably couldn't be arsed sending him back through the non-EEA queue when it became clear that I was not in fact exercising Treaty rights, but rather coming for a city break in Lisbon.