This is a very interesting discussion. Our Separatist and Puritan ancestors branded any displays of religious signs, symbols and statues, etc. as "popery".
True, but the longrifles weren't being built in or for New England, but by and for the PA Dutch and others for other PA Dutch and Scots-Irish/English, who were largely Presbyterians and other dissenters (non-Church of England). Those are different traditions with differing attitudes towards religious art, I think. Also, the First Great Awakening had a pretty big impact on the colonial society and beliefs - what may have been true of the 17th and early 18th century wasn't necessarily the case post-1760.
However, I don't think that there has to be any specific prohibition against religious imagery to explain why it doesn't show up. Case in point: Even today, in my own old-school Presbyterian church, you won't find much overt symbolism on personal objects (fish on cars, etc.) Some, but not much. There is no prohibition against it and it isn't even discouraged
per se, it just isn't how we tend to express ourselves.
The issue of church membership is an interesting one. I'll add my 2 cents: In the Carolina backcountry immediately prior to the Revolution, there were only a handful of established, formal churches. Only two or three Presbyterian congregations and the Moravians in Salem, plus a Quaker church or two, I think. If you only count those who were formally members of those churches, then the percentage of churchgoers in that region would appear very small. However, it is pretty clear from other sources that there were numerous people who were gathering together of a Sunday to read the scriptures and take turns preaching to each other - Quakers, Baptists, Presbyterians, and whatnot all in the same gathering. By the standards of the day, those would not have been considered as belong to a congregation; by today's standards they very well might. I think that there were church services being held in Boonesboro even from the very early days, though I am not certain.
I don't tend to think that everyone, or necessarily even a large majority, of folks were all that serious about religion. I suspect that it wasn't all that different than today, as a matter of fact. the way churches were established and tied into a larger system was different though, so just looking at formal membership is a bit misleading, I think.
Also, American attitudes towards religion seem to have changed quite a bit over the 70 years or so the longrifle was in its heyday. Might not be a good idea to generalize too much.