Totally. We just ran into this issue. Running npm install inside a linux vm resulted in an endless loop, because the nfs mapping created path names that exceeded the length limit.
NPM 3 tries, not entirely without success, to flatten the tree under node_modules/; I've had good results using it to resolve the kind of path length issues (in this case, with NTFS directories mounted in a VM) that you describe. Might be worth a look in your case as well.
