Short Answer
Assuming Freud is a short-hand for modern psychology of personality, then the difference between personality psychology and subatomic particles is best understood as the divide between soft and hard sciences. The philosophical problem of the demarcation of science tends to suggest that preference for hard over soft sciences is one of personal preference, though the physical sciences might be said to produce more certainty. In all cases, a central doctrine of modern sciences and arguably a key criterion for differentiating them from pseudosciences is their roots in fallibilism.
Long Answer
First, when you begin talking about the physical and the abstract, and deciding what exists, you are squarely in the realm of ontology. If you start laying out rules for existence, such as von Neumann's ideas or Rudolf Carnap's ideas, then you are engaged in metaontological discourse, that is, deciding what is the nature of ontology itself. The history of philosophy is one long debate about such metaphysical concerns.
Now, let's talk about Freud and science. First, while Freud was hugely impactful on psychology, by today's standards Freud is considered a bit pseudo-scientific. First, in Germany in particular in the nineteenth century, what constituted psychology and what the implications of that were was somewhat under contention. There was a movement called anti-psychologism in which a serious debate was had about the relationship of the mind to other entities, etc. The relationship of the mind to the body is a mainstay of philosophical discourse with mind-body dualism being a very famous position.
Secondly, the nature of science itself underwent a tremendous revision after Freud particularly in the form of a revolt against mind-body dualism, philosophical and psychological behaviorism, and a movement known as logical positivism which attempted to expunge metaphysical speculation from science altogether (and which failed). By today's standards, Freud is quite unscientific, as is a thesis of the book Why Freud Was Wrong. So, you've leapt right into a key philosophical struggle, deciding what is metaphysical explanation (SEP) which is a key part of philosophy. Modern psychology attempts to seat it's scientific legitimacy in operational definitions. The psychology of personality, the very essence of what Freud practiced, is today often associated with the five-factor model, for instance. Now, we are ready to address your question.
Would it therefore be fair to say that the difference between the (scientific) existence of subatomic particles vs id and super-ego comes down to their success in explaining reality?
Sort of, both the personality model and the sub-atomic particle are highly abstract, and neither are directly observable by the classic senses. In this sense, they are empirical, but as empirical evidence they are extended because they require tools and interpretation. But the major difference isn't one of scientific explanation, a notion itself open to philosophical debate. It's that one is physical and open to tensor analysis, and the other is mental and generally is understood as being rooted in statistical analysis. In fact, these are generally characteristics of the divide between the hard and soft sciences. Some philosophers place a primacy on things physical, and others on things mental. The dominant metaphysical presuppositions outside of theology in the analytical and Continental traditions does tend to be naturalist which roughly favors the certainty of knowledge in regard to the body.
Is one more scientific than the other? Well, for a long time, especially since physics comes out of natural philosophy, physics and Newtonian determinism were held up as the quintessence of rigorous science. Physical "particles" whatever they may be have historically been seen as objective, and human minds as subjective. And while physicalism is certainly the predominant and popular metaphysical view among professional philosophers today, idealism did have that distinction for quite a long time. In fact, these days, in the philosophy of science there is a still a tension between scientific realism and instrumentalism, so much so, one might be tempted to say that models of subatomic particles and models of personality don't describe reality so much as define it, a view popular with those who lean towards a naturalized epistemology and accept psychological and educational constructivism.