Right clicking a Skeleton (or a Wither Skeleton) with the respective Spawn Egg will make them unequipped, regardless of what item they must have...

How to reproduce?

Use the Spawn Egg of either Skeleton or Wither Skeleton.

Spawn one Skeleton or a Wither Skeleton, then Spawn another of the Skeleton of Choice while right clicking the first one.

The Results? The Second one does neither have a Bow nor Sword.