Materials and Preformance on a Massive scale...

Say you have 1,000,000 mesh cubes, 3 sides of the mesh are one material and the other 3 are a different material. Now say there are 1,000,000 pairs (2 mil total) of separate meshes with 3 sides, each forming half a cube with only one of two materials assigned to each game object. Performance-wise, which would be the best solution? Would it be even or would the increase in the total number of meshes offset the performance hit from multi-material meshes.( I hope I'm making a bit of sense.

Also, if one wanted to store a massive amount of gameobject (transforms and custom types and values), what would the implementation of this be? If you could point me in the right direction, I wouldn't mind researching the topic myself.