Let say I have a geometry having unnecessary vertices in vertex list. But those unnecessary vertices are not referenced in face list of this geometry. Will three.js make an extra calculation while rendering this geometry due to unused vertices or will it just ignore those vertices?
Three.js technically doesn't care about the contents of the vertex list. It uses that data to create a buffer, which it sends to the GPU. The same is true for the faces list.
The GPU will look at the faces buffer to determine which vertices to use to draw a particular face. If there are extra vertices in the vertex list, they should be ignored, but they do take up extra memory.
Take a look at how BufferGeometry builds its vertex list (BufferGeometry.attributes.position) and faces list (BufferGeometry.index). This is much closer to how GL and the GPU use these lists, and should give you a clearer picture of how the relationships work.