I wonder if it's more knowledge of the "outside" world, more interaction with people with those religions etc. So it isn't as "unusual" and "exotic" anymore. And of course there's more overseas markets for people who might be offended by it. Part of anime becoming more bland and boring... I think there was kind of an Asian chic thing going on in western media around the same time actually, funnily enough (games like Jade Empire and whatnot). Also a lot of that western occult/religious imagery has also become self-consciously a chuuni stereotype I think. When I see it these days it's usually as a joke about a chuuni character.

Which is why I feel like I still see this kind of thing in more doujin works. Although I can't think of many off the top of my head. It's not super recent but Rosenkreuzstilette and its sequel were excellent.