I actually noticed something like this yesterday when a buddy of mine used it, didn't seem to stun or damage several models. It could have been a fluke, but now that you're saying, it sounds weird.
You sure? I think it could also miss before. When I tested it vs. AI, it would sometimes hit retreating squads at around 100 range when they were already back in the base. Sometimes it would also miss.
Once my sniper hit the cover in front of him and stunned himself O.o
Oh and sometimes it would only stun half the squad when they were too spread out.
I like never used German Snipers because they die so fast. But this Ninja sniper sounds like a fun thing to try out. Maybe on my not so serious streaming days I will try this so called Ninja Snipers.