For example when one says something along the lines of $K_n$ is the complete graph on $n$-vertices what exactly are they referring to? An unlabeled graph or a labeled graph?
If its labeled then don't they have to specify $E(K_n)$ and $V(K_n)$ first?
If its unlabeled then is it an isomorphism class? If not then what it is formally?
Are unlabeled graphs not isomorphism classes of labeled graphs?
The math is more important than the formal description of the math.
Yes, if we're defining a (simple) graph as a pair $(V,E)$, where each $e \in E$ is a subset of $V$ of size $2$, then there are multiple graphs that are "complete graphs on $n$ vertices". So we could let $K_n$ denote the isomorphism class of complete graphs on $n$ vertices, and sometimes we refer to such an isomorphism class as an "unlabeled graph".
But in practice, it's convenient to make statements like "The complete graph on $n$ vertices has $\binom n2$ edges", and pretty much everyone does it when the vertex set is irrelevant, which is almost always. It would be more technically correct to say "Every complete graph on $n$ vertices has $\binom n2$ edges", but this statement is a bit confusing. It reminds us of the statement "Every tree on $n$ vertices has $n-1$ edges", but unlike the statement about trees, the statement about complete graphs doesn't actually need to consider multiple different cases. Once you've proven that one complete graph on $n$ vertices has $\binom n2$ edges, you know that they all do.
In actual usage, it makes the most sense to interpret $K_n$ as denoting an arbitrary complete graph, whose vertex set we don't care about, because everything we say will work no matter what it is.
P.S. I'd be careful about the word "labeled graph". This, in actual usage, can be understood to mean something like "graph with vertex set $\{1, 2, \dots, n\}$ for some $n$". For example: