The Huguenots who fled France following the revocation of the Edict of Nantes (which happened in 1685) were Protestant. The Edict of Nantes had offered them security but its revocation meant they were likely to be persecuted again. So during their initial period in Ireland at least, I would expect them to appear in Protestant records rather than Roman Catholic records, though judging by the 1901 census, any that remained in Ireland then had, ironically perhaps, apparently become Roman Catholic. In Ulster some became Presbyterians, because the Huguenots doctrine was closer to that denomination than the Church of Ireland.
There was a Huguenot church and a cemetery in Dublin (near St Stephens Green) for a while and the church does have some records. Might be worth checking those.
If you think that some of the families are of French origin but pre-date the 1600s, then a likely time of their arrival could be the Anglo Norman settlement of Ireland (1169 onwards). Many of those that arrived then were of French origin and had only lived in England for 100 years or less, having arrived in England in 1066 or afterwards. Some ended up settling in Ireland and after a few generations were regarded as native.
But tracing individual families back that far is not really feasible. Apart from documents for a few key leaders, there are no detailed records for the Middle Ages in Ireland. No baptism, marriage or burial records. In general the earliest records start in the 1600s but even that is very patchy, and it's the 1800s before most parishes have records. The Church of Ireland lost a lot of its records in the 1922 fire, but no RC or Huguenots church records were stored there. So they were unaffected by that issue.