• VSCode Version: 1.15.1
• OS Version: macOS Sierra 10.12.6

Steps to Reproduce:

1. Open Settings
2. Set color theme to Default High Contrast
3. Add color customization for the whitespace foreground color
4. Save your settings

Whitespace remains the default white color. Other settings (e.g. line number) are able to be overridden.

…
  "workbench.colorTheme": "Default High Contrast",
  "workbench.colorCustomizations": {
    "editorLineNumber.foreground": "#555",
    "editorWhitespace.foreground": "#555"
  },
…

Reproduces without extensions: Yes