[0 olszewski@macbookpro] /tmp/pnpm-prune-test $ tree
.
├── node_modules
├── package.json
├── packages
│   ├── a
│   │   ├── node_modules
│   │   │   └── b -> ../../../node_modules/.pnpm/b@2.0.1/node_modules/b
│   │   └── package.json
│   └── b
│       └── package.json
├── pnpm-lock.yaml
└── pnpm-workspace.yaml
[0 olszewski@macbookpro] /tmp/pnpm-prune-test $ cat packages/a/package.json 
{"name": "a", "dependencies": {"b": "2.0.1"}}
[0 olszewski@macbookpro] /tmp/pnpm-prune-test $ cat packages/b/package.json
{"name": "b"}
[0 olszewski@macbookpro] /tmp/pnpm-prune-test $ cat pnpm-lock.yaml 
lockfileVersion: '6.0'

settings:
  autoInstallPeers: true
  excludeLinksFromLockfile: false

importers:

  .: {}

  packages/a:
    dependencies:
      b:
        specifier: 2.0.1
        version: 2.0.1

  packages/b: {}

packages:

  /b@2.0.1:
    resolution: {integrity: sha512-JBWAj6f91ocNLbdg1jCGrxHXSWbQDsxgqVmKeO0TellEcq9LCvJ97iWG6p3otCt/v08/hHrWwAB9vNYS9y70IQ==}
    engines: {node: '>= 0.8.0'}
    dev: false