Back in the NES days games that were localized for American audience heavily censored any overt Judaeo-Christian imagery or reference to death. Churches no longer featured crosses, the Death spell was renamed to "RUB", and the Kill spell was renamed to "XXXX".

UFO 50 games notably don't really touch upon Christian stuff at all. Except one game - Grimstone. It's a very Final Fantasy-like JRPG set in Wild West except the continent somehow ended up in Hell itself. The local religion is very Christian-like with angels and holy water and and and BIGGAN!!

Interestingly, Grimstone shares its setting with two other UFO 50 cartridges - Devilition and Rail Heist but neither game feature that much religious references except for demons in the former.

Now, it can be just a coincidence but it's interesting to think about nonetheless.

Are you sure that was Nintendo's doing? Just off the top of my head, both Castlevania and Ghosts 'n' Goblins had religious imagery and references to death on the NES.

As far as I can tell the policy was established in the late 80s and lasted through the first half of 90s. Here's a relevant link.

There’s also a relevant quote from Wikipedia article on Actraiser:

According to Douglas Crockford's Expurgation of Maniac Mansion, Nintendo of America had a strict policy regarding game content in the early 1990s, especially in regards to material that could be deemed offensive, a blanket category that prohibited the inclusion of any overtly religious themes or plotlines in a game.

Nintendo of America may not have been consistent, but they were definitely over-strict for some games.