When Nicola gets round to showing Patrick the details from the farm log about the martyred Merrick ancestor, he says something along the lines of how odd it is, that every time he's decided the whole thing (ie his faith) is nonsense, something like this always comes along to make him reconsider. So I think it's clear that in those later books - when he is, presumably, around 17 - he is, as one would expect, experiencing a very normal stage of doubt and questioning, whereas in the earlier books (also, in a pscyhologically rather convincing manner) he is as deadly certain and priggish as early adolescents generally are about their beliefs (whether religious or otherwise). As for Nicola, it is made quite clear I think when she goes to Mass that she finds it a deeply religious experience, one which she would rather not repeat precisely because she found it overwhelming. So I think the religious/non religious lines are a bit more blurred than you suggest here as the children grow up.

Patrick is often sensitive and resourceful in his dealings with others. It is true that he is not often kind in a particularly creative or thoughtful way but in my experience that is very typical indeed of intelligent only children, and perhaps especially of boys. There is a kind of everyday thoughtfulness (about bathwater, television sharing and so on) which is an essential part of being one of a large family, and is quite alien to a well-off only child.