When you think about it it they come up in real life as well, just you aren't necessarily aware of them. Wouldn't it be strange, for example, if you measured the distance between two atoms and it turned out to be exactly 1 metre? Or an exact fraction like 1.4 metres? Or even a long fraction like 1.453162343055682m? It seems much more likely that the number would be an infinite series of random-looking digits, which would make the distance an irrational number.
That assumes a naive model for the universe in which we live. The distance between two atoms is not a number that can be determined with arbitrary precision, so it doesn't make a lot of sense to ask whether it is rational or irrational. I am not a physicist, but my understanding is that this is not just a limitation of our instruments, but a feature of nature.
The way I think of the world these days, everything that matters is discrete. Real numbers are a convenient approximation in situations where the numbers are large enough. This is often the case in physics; but there is nothing "real" about real numbers.
Yeah, fair point, I was assuming a simple Newtonian / Euclidian universe - just trying to build up some kind of intuition about what irrational numbers are.