I don't think we do anything that would increase latency for API clients specifically.
But if your API is not implemented on the edge (e.g. in a Worker), and the responses are not cacheable at the edge, and you aren't using Argo, then there's not much else Cloudflare can do to make the request faster. Cloudflare is just proxying requests at that point, and the presence of a proxy will indeed probably add a few milliseconds of latency vs. the client talking directly to the origin. (Of course, you do get other benefits like DDoS protection.)