I thought that was due to the myth of using praying to get quality items.
It was in one of a town's forum.
I have no idea what you're trying to say here since it's completely out of context with the quote that precedes it, but surely nobody actually subscribes to that theory about prayer improving shop items anymore. I haven't seen widespread support of it since about 2010, and there's no substantial evidence to back it up, though I suppose there's no harm in continuing to try if you're superstitious.
I was told that praying "can never hurt" but that INNO will not confirm or deny that it does anything to help you with the game.
Actually, praying allegedly does have a negative effect if overused, kind of like the bell curve that affects the aim and dodge skills in duels. I doubt anyone will ever see such a negative effect since in the last eight years nobody has been able to identify the positive one, and to trigger such a negative effect would presumably require quite an excessive amount of praying.
EDIT: As to the actual idea itself, while it would be nice to make building seem a bit more meaningful, I doubt we'll see anything further in that regard simply because Inno have stopped developing new features. Perhaps some small changes could be feasible, but no major ones like entirely new buildings (railroads and railway stations have been suggested about a thousand times over the years, by the way... the concept never seemed to appeal to Inno). Anyway, there's hardly a shortage of builders around with church building being arguably the best source of exp.