As @Gaël J suggested, the more appropriate option is to use 'matchCurrentVersion'.

renovate.json:

{
  "$schema": "https://docs.renovatebot.com/renovate-schema.json",
  "extends": [
    "config:recommended"
  ],
  "packageRules": [
    {
      "matchPackageNames": ["chalk"],
      "matchCurrentVersion": "/java$/"
      "enabled": false
    }
  ]
}

This now disables the check and subsequently disables the generation of the PR:

"deps": [
  {
    "depType": "devDependencies",
    "depName": "chalk",
    "currentValue": "2.5.2-java",
    "datasource": "npm",
    "prettyDepType": "devDependency",
    "updates": [],
    "packageName": "chalk",
    "skipReason": "disabled"
  }
],