Catholics pretending to be Protestants in Ireland?

[Maiden Stone]

I'm going purely off of what I have heard from my mother...they were both Catholics, on the census too....but they were for some reason married in a Church of Ireland Church in Dublin...the children were raised in that faith as far as I know, with classic Irish Catholic names...they were all born and raised in County Wicklow

When was the marriage and when were the births?
Both civil laws and religious requirements regarding marriage were a bit confusing in Ireland in 19th & early 20th century and they changed during that period. That's why we can't try to answer your questions with confidence unless we know when events occurred.
Have you considered that your great grandparents may have had a later wedding ceremony in a Catholic church? 

Added. Which census? Was it when they were a married couple? How long did they say they had been married?

 

[Maiden Stone]

...they were both Catholics, on the census too....but they were for some reason married in a Church of Ireland Church in Dublin...the children were raised in that faith as far as I know, with classic Irish Catholic names...they were all born and raised in County Wicklow

Was it the Long -McIntyre wedding at St. Paul's, Dublin in 1925?
Threads about the family with marriage certificate on one and link to it on another.
https://www.rootschat.com/forum/index.php?topic=768661
https://www.rootschat.com/forum/index.php?topic=768771
https://www.rootschat.com/forum/index.php?topic=768798
https://www.rootschat.com/forum/index.php?topic=768802

I think it has "by licence" handwritten. That suggests to me that the wedding was arranged quickly. 

[Sinann]

...they were both Catholics, on the census too....but they were for some reason married in a Church of Ireland Church in Dublin...the children were raised in that faith as far as I know, with classic Irish Catholic names...they were all born and raised in County Wicklow

Was it the Long -McIntyre wedding at St. Paul's, Dublin in 1925?
Threads about the family with marriage certificate on one and link to it on another.
https://www.rootschat.com/forum/index.php?topic=768661
https://www.rootschat.com/forum/index.php?topic=768771
https://www.rootschat.com/forum/index.php?topic=768798
https://www.rootschat.com/forum/index.php?topic=768802

I think it has "by licence" handwritten. That suggests to me that the wedding was arranged quickly. 

I was just about to post the same, don't know where they are in the census though.

[Dannyboy20]

http://www.census.nationalarchives.ie/pages/1911/Dublin/Arran_Quay/Phibsborough_Road/48555/ this is I believe my great grandmother Mary, as my grandmother was Grace Frances...my great grandfather John Joseph I am seeming to have difficulty finding...there is one in Arklow on that website but he died in 1943 aged 57, I have his death certificate.

[Kiltaglassan]

http://www.census.nationalarchives.ie/pages/1911/Dublin/Arran_Quay/Phibsborough_Road/48555/ this is I believe my great grandmother Mary, as my grandmother was Grace Frances...

So, your gt grandmother was Mary Frances McIntyre aged 13 in the 1911 census, and living in Phibsborough Road (Arran Quay, Dublin).

Here's her birth record-  MMN Delaney
Born 21 August 1897 at 6? Grattan Parade, Dublin.
https://civilrecords.irishgenealogy.ie/churchrecords/images/birth_returns/births_1897/02107/1802125.pdf

[Dannyboy20]

That's right, and thankyou for the additional information! This here is my great grandfather John Joseph's death certificate
https://civilrecords.irishgenealogy.ie/churchrecords/images/deaths_returns/deaths_1943/04656/4238936.pdf at the bottom, Knockanree, Avoca.
It's very puzzling to me to say the least this whole thing! He's the one I have trouble finding, it says he died aged 57 in 1943.

[Sinann]

I'm reading the marriage cert as saying her father is Stephen.
https://civilrecords.irishgenealogy.ie/churchrecords/images/marriage_returns/marriages_1925/09139/5305477.pdf

[Dannyboy20]

That's also another thing that I can't work out...could her father have died and maybe Stephen, an uncle signed it?

[Sinann]

Doesn't matter if her father was dead or alive he has to be named on the cert unless he is unknown, no one else can be named in his place.
People who didn't know who there father was might make up an name.