I don’t think there’s any reason to believe that, say, the fine structure constant, or the ratio of the mass of a neutrino to the mass of an electron, are rationals, or even algebraic.
Maybe there is though? That seems like very much a question for philosophy, since scientific measurement will never be able to tell us for certain.
Hence, rationals are plenty sufficient for all of physics, assuming you bother to reformulate all the theories that are historically based on real numbers. However, there is no point in doing this, so only a few niche people try (who, of course, do it for philosophical/aesthetic reasons).
No matter that physical reality insists that the number of people in a population or U-238 atoms in a lump of metal has to be an integer, mathematics will tell you that that integer nonetheless has a distinct, nonalgebraic natural logarithm, and that that number is useful in predicting how many people will be in that population or U-238 atoms will remain in that lump of metal at some later time - even if the raw result of any such calculation will be a nonsensical noninteger.
Hypothesizing that space & time are discrete is more difficult.
That literally doesn't matter one way or the other in the slightest, for two huge reasons:
1. No mathematics is exactly the same as reality itself, and cannot be, even in principle. Mathematics can be used to useful model certain limited aspects of reality, but of course models aren't the same as reality.
2. The mathematics of the reals and of continuity in general are essential for a vast number of kinds of practical computation that sometimes (not always!) turn out to be vastly harder to do without the assumption of continuity. We often want to bring to bear the whole apparatus of established mathematics to solve problems in order to get answers, and no one trying to get answers cares whether the mathematics used is "real", only whether the final answers are useful (accurate etc).
Actually there's a third reason that is even more important to some people: this is usually merely about word definitions. Words like "real" and "exist" have sharply defined unambiguous technical definitions in mathematics that are only indirectly related to the loosely defined vague non-technical definitions of the same words that we use in natural languages like English.
It is ultimately irrelevant whether e.g. the real numbers "exist" in the physical universe, because whether they do or not, they provably exist in (most) formal mathematics -- the word "exist" does not have the same meaning in the two realms.
It's still interesting to ask whether the physical universe has reals or continuity or infinities or infinitesimals etc., it just shouldn't be confused with the issue of their technical existence (or "reality") in mathematics.