> Do things 'go through' the vacuum of space or is it like newton's cradle where the fundamental building blocks just bump shoulders yet do not move?

You mean, is motion an illusion, much like a glider in Game of Life seeming to move?

Yea, are we just living in an enormous three dimensional grid or are there true vacuums in space?

One thing to consider, is that given rate of change approaches zero as velocity approaches c, what does motion mean when there is no time for it to happen in, either as things moving or bumping?