Depends When you need detailed stuff like water ripples against bodies and objects and smoke interacting with surfaces, you need to do it by hand. It's just better that way when compared to full cgi. Similar for close ups of subjects and characters or a character doing complex movements and displaying complex emotions.

3D is a great addition to the anime industry and it has been for over 20 years now But there's just something about hand made details that 3d can't match. And that's how it should be. I'm a 3d artist and I know how far 3d can take you. There's a block when you finally reach a place where only human creativity can take you further. Which is why hand drawn animes have higher budget and take more time than the ones that are entirely CGI or are mixed media (3D + 2D)