Edit: I'm trying to address Gerhard Paseman comment:
Let me start with this space of "generic real number" $G \subset \mathbb{R}$ defined as the intersection of all subspaces of density $1$ that I mentioned at the end. (Note to the experts:I am always confused on whether this space is already boolean or not, I'm assuming it is, but if it is not please tell me. If it is not then some of the things that I say below might require to move to a certain Boolean cover of $G$)
It has some quite nice properties that are easy to explain: For example bounded continuous functions from ${G}$ to $\mathbb{C}$ are exactly the same as element of $L^{\infty}(\mathbb{R},\mathbb{C})$.
The fact that $G$ has no points simply corresponds to the fact that you can't evaluate a function in $L^{\infty}$ (in localic terms: these are functions defined only on generic reals)
more generally things defined over it are things defined "almost everywhere" and that for example one can define what are bundle of Hilbert spaces over $G$ and under countability condition they are exactly the same as measurable fields of Hilbert spaces on $\mathbb{R}$ with morphisms between them being already defined up to equality almost everywhere.
But the notion of bundle of Hilbert spaces over $G$ makes sense without countability conditions and is considerably more robust than the notion of measurable fields of spaces when we drop the countability assumption (it is equivalent to the notion of $W^*$-modules over $L^{\infty}(\mathbb{R},\mathbb{C})$ ).
But of course, all those require first to show that $G$ is non-empty.
An important applications of $S$ is for forcing in set theory. Though forcing existed before this kind of consideration this gives a very nice geometric picture of what forcing is (and this is completely equivalent to the usual formulation of forcing, its just a different language).
Essentially, by replacing "sets" with "sheaves over the Space $S$" (or more precisely, over some boolean cover of $S$, or looking at double negation sheaves) one obtains a new model of set theory in which $I$ is actually countable. This is what Set theorists call a forcing extension that collapse $I$ and $\omega$.
informally (though it can be made formal with things like internal logic) its because working with sheaves over $S$, means working with structure which depends on a parameter $s \in S$, and informally such a parameter is the data of a surjection $\mathbb{N} \rightarrow I$
Other kind of forcing corresponds to other space similar to $S$, and one generally proves they are non-empty by the same argument.
The fact that space $S$ is non-empty is really equivalent to the fact that one can collapse cardinals by forcing, so it is a bit hard to find application outside of logic. But I'll see if I can think of something nice enough to be explained here.