it may look graphically simple

Because it is graphically simple. That's not even a CPU issue.

millions of blocks in memory at any time and has to cull which to not render, etc).

128x128x128 is already 2 million voxels. Minecraft and any other game like that can use an octree or some variation to not individually deal with blocks. When things are in the distance or occluded or empty space you cull a courser level of the octree.

Java can be fast compared to scripting languages but I don't know why minecraft would be an example. It is a simple game that was poorly written and had to be re-written in C++ for other platforms. It got by on being simple and but running on full PCs at the same time.