I think there is a flaw in your logic here. The physics we know has certain features-e.g. unitary evolution. But, it is possible that there is a “deeper level” of physics we haven’t discovered yet. There are some major proposals for what that “deeper level” (or levels) might look like - e.g. M theory or loop quantum gravity - but for all we know maybe the underlying “real physics” is something nobody has even thought of yet, maybe something completely out of left field whose discovery is centuries away.
Whatever that “deeper level” is, should we assume it shares the “surface level” features such as unitary evolution? Well, there are two possibilities (a) yes it does (absolutely or universally so), or (b) in the most general case, no it doesn’t, but in the normal situation those features emerge.
Suppose, in the “ultimate physics”, unitary evolution is actually violated, but only at very extreme energy levels we are nowhere near being able to test? Or maybe it is conserved locally, but in distant regions of the universe (say a googolplex parsecs away) it isn’t? Or maybe it is conserved in the present, but in the very distant future (say a googolplex years from now) it won’t be any more? Do we have any way of knowing those possibilities won’t turn out to hold?
But if we don’t, then using the fact that cellular automata lack that feature as an argument against Wolfram’s hypothesis - it seems to me rather weak. That’s not to say that his hypothesis is actually true - I’d be rather surprised if it were. But I just don’t think this is a very convincing argument against it