Why are church ninjas so common in anime?

In the examples you give, both are fighting secret wars involving the supernatural.  Why covert?  Because vampires and mages and "actually King Arthur had boobs" are secret.  Why super soldiers?  Because fighting vampires and mages and waifu King Arthur.


As for why the Japanese might view Christianity as an organization that has a secretive militant side to it?  It was historically banned in Japan but the Church refused to leave and instead went underground.  

Christianity has little presence in Japan so it is treated more as an aesthetic than a religion. Nuns in particular get treated like a palette swap of mikos, who are also commonly converted into warriors fighting against demons and other threats.

Well, a lot of it are Hellsing references but overall they just see Christianity as a cool and foreign religion, and I can get it. It has a lot of aura at times.

It's just monks with a different religion

./curious, yet ready-to-kill Roberta noises intensify/

Let's see... dresses mainly in black, wields a lot of power while purporting to be common, and they overhear all your deepest secrets (confessional)...

the church is ninjas. it's a lock.

The short and simple answer is that's just what the genre has evolved into. The exorcist genre (which doesn't always dress up in christian regalia) has escalated to the same level of power creep as the rest of the battle genre. It's all characters blasting off tactical nukes while running at light speed. How it's dressed up doesn't really matter.

You are asking the wrong question. The question should be why not?

Why? Vampire Nazi's.

Because it's cool