I want to state something in a clear short post:
Minecraft isn't real life.
In real life, you make a microscope to see if animals have cells.
In Minecraft, you simply assume they have cells.
Minecraft tools will never be enough to confirm any of our theories.
In real life, we create electron microscopes to confirm the existance of subatomic particles.
In Minecraft, we look at a block and say: "It's divided in blocky things, must be some kind of particle"
We can't know if Blockules are 3D. We slice a block with a saw to see its insides. Instead, magic cracks appear and the block turns into a pebble.
We can spend our entire lives on this, but unless Mojang lets us have electron microscopes in Minecraft, or if They actually ADD all of our Hypotheses, we can't prove them.
I don't fully agree with this, only partially. I agree that evidence is limited in Minecraft, but that doesn't mean we can't come up with well founded theories. Again, I want to go back to Quantum Theory in real life. We have no direct evidence of anything quantum theory predicts. None. No one has ever seen an electron in a microscope, in fact, the concept of "seeing" totally breaks down at that level because now the fact that you have to use photons to "see" means you really can't see things that are the size of photons (which btw are another "unproven" thing). The reason we use quantum theory though is because it explains what we see around us so well. Heck, we're building computers using physics that, again, has zero direct proof.
So just because we can't "prove" a theory doesn't make it less valid, so long as it explains the world and the phenomena we see.