You will take a slight performance ding, since you’ll be pushing extra polys in the engine. You’re still instancing the textures though, and all instanced object draw on the same texture file.
Your question is a little confusing though - are you animating the 2 objects in Unity, or in Blender? If in Blender, you should just be able to export the 2 meshes as one object, along with the animations and armatures, right into Unity. If you’re trying to animate in Unity, I believe that will be less efficient.
Take this with a grain of salt - I’m much less experienced with Unity than I am with the UDK, but most of this stuff is pretty basic, and should carry over from one engine to another.