Cellular automata are used in physics, no less a physicist than Gerald t'Hooft proposed they can be used to interpret quantum mechanics, with the potential to unify physics and fulfil Archibald Wheeler's ambition to generate an 'It from bit' picture of the laws of physics emerging from something simple.
Stephen Hawking gave a lecture Gödel and the end of physics in which he suggested the mission of unifying physics may always have been hubris, and that there will always be unanswered questions.
We have good indications that quarks are point-particles like electrons, that lack any internal structure. But, String Theory, Quantum Spin Lattice Networks, or other structure could be hiding below what we can detect. I'd say the implicit premise of what you are asking is, can the layers go on forever, and that is called fractal cosmology, which we discussed here What would a fractal universe tell us about Time?
The basic job of a physics theory is to simplify or make more efficient our model of the world. This is why symmetry is so important, it is the core mechanism to shed unnecessary information, and by Noether's theorem we know conservation laws directly relate to this. For it to reduce to 'ultimate simplicity' of rules, requires that it has been ultimately simple at some time, and complexity emerged from there. Conformal Cyclic Cosmology is a nice proposal for cycling between simple and complicated, where we could imagine a 'random walk' selecting a set of fundamental physical constants each cycle.
We have reason to expect a fundamentally unified quality to things in our universe, because of the Big Bang. It all started in as close to one place, at one time, as it's possible to be. If the laws of physics are emergent, and causality not fully deterministic, we may not be able to get all the laws, but we will be able to understand where the ones we know come from, and tell the story of the emergence of what we have. For instance our universe could be a random fracture plane in the E8 hyperstructure.
Another possibility is the universe itself will turn out to gave a mind-like structure to it, transcending Godel Incompleteness and the halting problem in the same strange-loop way our minds are able to form tangled hierarchies and feedback. And minds involve irreducible complexity, to fully understand them you have to be them.
So the answer to all three questions is no, we can't be sure. But physics has been on a 'unification journey', as discussed here Is the idea that "Everything is energy" even coherent? which we have reasons to think will include minds Is it the job of physics to explain consciousness? linking them at least narratively with whatever the simplest state of the universe has been.