The fact that there is something that makes up atoms just means people jumped the gun when we gave what we called atoms their name. The principle Truth remains True that there is some sort of building-blocks that compose the universe.
If something is true, time and time again, then it is True. That's how these laws of physics, nature, and morality all work. Without having Truth, we have no progress. Because if there is no true north, then there is no way to find direction. If there is no Truth, then there is no order. But as long as there is order that we can comprehend and use to our advantage, there is Truth. You can call it a useful convention if you'd like, but as long as there is a law that exists in nature you cannot disprove, it is considered Truth.
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But that's just a convention we've come to see as useful because, like you said, it has shown to be useful over and over (again, by convention).
I'd say without shared consensus on useful conventions, we don't have progress. There have been inaccurate scientific claims in the past which still brought about progress because as more people used them, we eventually found flaws and improvements which led to even better conventions and new discoveries.
We only "prove laws in nature" by our shared conventions such as the scientific method. We find direction based on how effective our epistemology is for predicting future events and describing physical reality as we observe it.