I’ve seen cases before where some of the Composer autoload files were so big, they exceeded the 1 MB size limit for PHP files, resulting in them being discarded on upload. You may want to check the size of the missing files on your own computer to see if they are bigger than 1 MB.
If this is the issue, then you maybe able to reduce their site by reinstalling the Composer dependencies, but without the -o or --optimize-autoloader flags. The optimized autoloader file can be quite big, and you can avoid it that way.
As for the node_modules, you don’t need them here. The node_modules are only used while building the frontend code. They are development files and don’t need to exist on a live server. They are a waste of disk space here because you can’t build the frontend here anyways.