Yes, this is a problem. Someone should code something in C++, something like a videogame 3d engine accelerated by the GPU, this way you could be able to deal with massive amounts of blocks in 3d. Most of these javascript stuff is a mess for this. Maybe just use the Unity engine which works well in browsers. Unity has a built in plugin to import your work in a website easily.
I don't know about to study the 3d mappings. Right now it doesn't have much data, it's just a fancy way to view the network afaik. Raw data is better for research.