I do not know of an automatic way of reducing the number of files in node_modules (which is where npm stores its dependencies.) However, I can think of some options to reduce the inode use.
1) If there are shared dependencies (of the same version-number) between these projects, you can symlink some dependencies from one project into the other. If you get a dependency with lots of nested dependencies, this can really save quite a few inodes. (untested)
2) Another alternative, if there are lots of shared dependencies, would be to copy the node_modules of project 1 to project 2 with cp -l. In this case each copy would be a hardlink to the same file, not using any additional inodes. After that, run npm install && npm prune in project 2 to download any changes / additional dependencies. (also untested)
3) However, both options are hacky, and might or might not give you hard-to-debug problems later, after copy-ing, after restoring a backup, etc. The real solution would be to re-create the filesystem with more inodes. For ext4, this can be done with mkfs.ext4 -i . See https://unix.stackexchange.com/questions/26598/how-can-i-increase-the-number-of-inodes-in-an-ext4-filesystem .
