In the book Naive Set Theory, Halmos mentions that the "The least exciting relation is the empty one." and proves that the empty set is a set of ordered pairs because there is no element of the empty set that is not an ordered pair. Since the empty set is a set of ordered pairs, it follows that it is a relation.
I understand this line of reasoning but couldn't I use that same line of reasoning to prove that the empty set is a set of singletons? And since the empty set is a set of singletons (because it contains no elements which are not singletons) it is not a relation (because a relation is a set of ordered pairs, not singletons). Why is this reasoning invalid?
There’s no actual contradiction here. Let $A$ be any set, and let $S=\big\{\{a\}:a\in A\big\}$, the set of singletons of elements of $A$. Then $\varnothing\subseteq S$, so $\varnothing$ can be described (somewhat confusingly) as a set of singletons, but this is so vacuously: it’s a set of singletons because it does not contain anything that isn’t a singleton, not because it actually contains any singletons. Similarly, $\varnothing$ is a set of ordered pairs of elements of $A$, but only vacuously so, in that it does not contain anything that isn’t such an ordered pair. In fact, if $X$ is any set, $\varnothing$ could be called a set of elements of $X$, simply because $\varnothing\subseteq X$, but this is only vacuously true. It’s best just to notice that $\varnothing$ is a subset of every set and not to try to talk about the nature of its (non-existent) elements.
In particular, it’s better to say simply that every subset of $A\times A$ is by definition a relation on $A$ and then note that $\varnothing\subseteq A\times A$.