Yes, unfortunately, Kurama passed away in the manga. This occurrence brought about a lot of changes and emotions for both the characters and the readers.
Ni Mantian of Hua Qiangu died in the end. He had been killed by Bai Zihua during the final battle. To be more specific, Ni Mantian had always had complicated feelings for Hua Qiangu during the emotional entanglement between Bai Zihua and Hua Qiangu. However, in the final battle, in order to prevent Hua Qiangu from obtaining the power of immortality, he had sacrificed his life to fight with Bai Zihua and was eventually killed by Bai Zihua.
For Naruto, it would be a whole new experience. He'd be constantly trying to communicate with the mecha Kurama, learning its quirks. Shikamaru might be the one thinking about the strategic uses of mecha Kurama in battle. He'd be coming up with plans on how to best utilize it. As for Kurama, he could be in an internal struggle. Part of him would want to stay relevant in Naruto's battles, while another part would be curious about this new mechanical version of himself and how it could help Naruto in the long run.
The shadow in Qing Yuannian's novel did not die in the end. In the final battle, the Shadow, Fan Xian, Wu Zhu, and Fan Ruoruo joined forces to assassinate the Qing Emperor. Although the Shadow, Wu Zhu, and Fan Xian were all heavily injured, they all managed to keep their lives and left Jingdou together. Therefore, the shadow did not die at the end of the story.
The shadow in the novel did not die in the end. In the ending of the novel, the Shadow was stabbed by Ye Chong in the Battle Palace, but did not die. He, Fan Xian, Wu Zhu, and Fan Ruoruo had assassinated the Qing Emperor together. Although they had suffered serious injuries, they had managed to preserve their lives and leave Jingdou. Therefore, the shadow did not die at the end of the story.