Dependency install times went down by a huge amount, and all the strange issues we had with lerna and npm sometimes erroring out, requiring us to remove all node_modules folders and re-install everything, are just gone.
We even noticed that the size of some of our production bundles went down. Before some dependencies that were used in multiple packages were being duplicated in our webpack bundles needlessly, but the way pnpm symlinks dependencies instead of duplicating them fixed that as well.
The non-flat node_modules structure did break some things as well, since in some places we had imports pointing to packages that were transitive dependencies and not defined in package.json. I see this as a positive though, since all those cases were just bugs waiting to happen.