Note: This FAQ item refers to Witch's built-in icon badge overlays, not badges from Mail.app (which is presently the only third-party app whose badges appear in Witch).

If you're not seeing the shortcut (0, 1, 2, etc.) badge overlays in Witch's panel, it's because Witch doesn't have enough room to display them, based on the current setting of the Item Size slider (on the Appearance tab). The limits are different for application badge overlays and the others:

• Space number and keyboard shortcut overlays: Item Size must be 19pt or larger.
• Application badge overlays: Item Size must be 32pt or larger.

Change the Item Size slider to at least 19pt or 32pt, and you'll then see the respective overlays.