Wikipedia shows this schema and calls it a "schematic representation of a category":
I have seen these types of schemas often in contexts where the word "category theory" is not mentioned at all. For example, where $X$ is $R^d$ and $Y$ is $M$ (a manifold). Now I am not at all knowledgeable about category theory, and I only stumbled upon this scheme by accident, realizing I've seen them many times before.
Does this mean that I have been "working" with category theory all along without knowing it? Are all these types of schemes actual implicit applications of category theory, or are they also used in "non-category-theory-ways"?

Those diagrams, as they're called, come up way more often in category theory than anywhere else. But as the goal of category theory was generalization of many (if not all) mathematical concepts, it's perfectly normal to stumble upon those diagrams even when working outside of category theory. You could say they're implicit applications of category theory, but imo that would be far-fetched, it's just that diagrams are, more often than not, the "natural language" of mathematics