For a common basis, I'll state basic definitions of a category and the relation type I'm thinking of. They're here for quick clarity, not precision, so feel free to revise for an answer.
Category:
A collection of objects, a collection of arrows each with a source and target among said objects, identity arrows, and a composition operator satisfying an associative law over arrows.
Reflexive relation on AxA:
A collection of objects, a labelled multi-set of pairs of said objects satisfying the reflexive law, and the standard relation combinator operation (which satisfies the associative law).
Note that labelled multi-set relations are commonly expressed and utilized in discrete math as multi-graphs. I collapse graphs and relations here for unified axiomatic treatment. This is not to treat, e.g., paths over graphs as different from relation composition.
What, exactly, separates these two? They appear essentially identical in definition and meaning to me. Relations immediately appear more general, given that categories only analogize to a certain restricted class of relations.
I note some notational difference, such as how categories name each arrow; I don't see how that would change mathematical power. Similarly with the explicit treatment of composition. While such contrivances can come in handy for certain proofs or explorations, I don't see how it justifies treating the two as separate branches rather than syntactic shims on identical concepts.
[EDITS: fixed associativity statement, extended relations to multi-set representation with graph analogy]
A directed multigraph can be thought of as a one-dimensional simplicial complex: the vertices are points, and the edges are 1-simplices.
Given a category, we can form its nerve, and the 1-skeleton will essentially be a multi-graph.
The observation of the OP is that these two constructions are roughly inverse to each other.
The relationship between simplicial sets and categories is an important one, and is at the basis of the theory of higher categories and its relationship to homotopy theory. Thus the OP's observation and question shouldn't be dismissed.
On the other hand, I'm not sure that I agree with the sentiment of the OP's final non-parenthetical sentence: "I don't see how it justifies treating the two as separate branches rather than syntactic shims on identical concepts." Certainly (multi-)graph theorists and (higher-)category/homotopy theorists both make itensive studies of 1-dimensional simplicial sets, but the questions they ask and the constructions they are concerned with are typically extremely different. If they do find common ground, that's great, but they needn't be obliged to seek it.
Most working mathematicians using categories are, furthermore, not thinking in a homotopical/simplicial way at all about the structures involved, but are just taking advantage of the very useful language and range of concepts that category theory provides. These are concepts that (as far as I know) are not used at all by those studying multi-graphs and related structures, and so I don't see any reason that people should be obliged or even encouraged to translate (what to them are) familiar category-theoretic notions into a different terminological framework of relations/multi-graphs.
[Added: Ryan Budney's comment above makes essentially the same point in a pithier fashion.]