The location reference in the first column of the baptism register is the family residence, e.g. Moneytucker for Thomas in 1857, Mary's maiden surname is noted as Doyle, the parish is Davidstown, which is to the west of Enniscorthy Catholic parish. You can view the register entry for Thomas on the National Library of Ireland website - it's the second last entry on the right hand page. Bridget's baptism record confirms mother's maiden surname, and gives the same residence.
I don't see any likely matches for a baptism for John, and there doesn't appear to be any significant gaps in the Davidstown registers. Maybe John was born and baptised in another parish that doesn't have records for the time he was born ? It's quite common to come across missing sections, or badly faded or damaged pages in registers which could also account for the difficulty in locating a record. A search for marriages of a James Ryan and Mary Doyle show quite a few results, as you would expect with such common names, but none in the Enniscorthy area around the right timeframe.
There were two chapels in the parish in the early 1800s, one at Davidstown and a second at Courtnacuddy townland to the west, the baptism probably took place in the parish church, which would likely have been the one at Davidstown.
