Not an actual ninja but Finik at least has the vibes of one despite using guns & grenades. Not sure how popular though. https://steamhost.cn/steamcommunity_com/sharedfiles/filedetails/?id=2219848760 As for Japanese themed characters, there's Ayaka Kinoshita. https://steamhost.cn/steamcommunity_com/sharedfiles/filedetails/?id=2802914735 Oh yeah, here's a popular ninja. https://steamhost.cn/steamcommunity_com/sharedfiles/filedetails/?id=2404624900 Lonin & Mio are more like Samurai, I guess? https://steamhost.cn/steamcommunity_com/sharedfiles/filedetails/?id=2302675649 Opengunner has a lot of Japan-themed characters. https://steamhost.cn/steamcommunity_com/sharedfiles/filedetails/?id=2605304929 https://steamhost.cn/steamcommunity_com/sharedfiles/filedetails/?id=2820380997 https://steamhost.cn/steamcommunity_com/sharedfiles/filedetails/?id=3032623758 https://steamhost.cn/steamcommunity_com/sharedfiles/filedetails/?id=3133046076 https://steamhost.cn/steamcommunity_com/sharedfiles/filedetails/?id=3139861907 https://steamhost.cn/steamcommunity_com/sharedfiles/filedetails/?id=3397891986 I'd say Reimu & Miko qualify since they're shrine priestesses.
https://steamhost.cn/steamcommunity_com/sharedfiles/filedetails/?id=2263955842
https://steamhost.cn/steamcommunity_com/sharedfiles/filedetails/?id=2089363375
Mamizou Futatsuiwa's a tanuki.
https://steamhost.cn/steamcommunity_com/sharedfiles/filedetails/?id=2854485508
Edit: Also, here's a character based on Strider Hiryu.
https://steamhost.cn/steamcommunity_com/sharedfiles/filedetails/?id=2500822911
Also, I forgot Naruto.
https://steamhost.cn/steamcommunity_com/sharedfiles/filedetails/?id=2802388684