That's because the term was adopted as one of the running gags for Ninja Slayer. When you see it used as an exclamation in most manga like this, in association with the presence of a ninja, it's a Ninja Slayer reference. See here and here.
If you trace backwards, she was a real ninja attached to the Oniwaban which were guards of the inner garden.Ninja!!What's wrong?She's really a real ninja!?Sendai was formerly a ninja employed at the Imperial House of Japan.What are you saying, Nowaki?Commander... A lie like that would be found out straight away...Sendai is a ninja.... You can't mean Sendai?Sure she sort of looks like one.Ni... Ni...Huh? Look I'm sayin'... Oh yeah, Nowaki didn't know about it.Huh!?The early afternoon~ was reflected~ in your~ glittering eyes~lyrics from Tactics "Rurouni Kenshin"They really existed!!Gauranga! I'm touched!!
