How can I build/deploy my Website with THREE.js with multiple html files

you would typically use what is called a router instead of multiple html. this is called SPA (single page app). or you use a dedicated service like nextjs instead of vite, there you have file system routes and it is probably very close to what you already have.

edit:
found this, vite also supports multiple entry points vue.js - Multiple entry points in Vite - Stack Overflow