I would have to say yes, through logical and mathematical arguments, through philosophical arguments... but not through empirical science for reasons already clearly explained.
Mathematicians do it all the time. You can prove the non-existence of a largest prime number, for example. That is just one special and famous case of proofs of non-existence using logical arguments.
This sort of reasoning - proof by contradiction, and other forms of proof - can extend to any facet of existence, any claim, if one can create a model to which this sort of reasoning can be applied.
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Just because one cannot disprove the existence of something does not mean it exists. I agree with that statement. But just because one cannot prove the existence of something does not mean it doesnt exist, either. The universal generalization of the claim that something doesnt exist is no less fallacious than claiming something does exist without the proof, and vice versa. Fact is, in many cases its absurd to even discuss the topic because it is outside of the realm of rationality. Any claim, whatever it may be, demands proof. Believing anything, anything whatsoever, without a rigorous proof of it, is nothing short of faith. And there is nothing wrong with faith. Faith is the foundation of everything. The axioms of reason. The postulates of geometry and of arithmetic. The very principles of empirical science itself cannot be proven. All are taken on faith. The only real issue - the only real problem - is when someone is unwilling or incapable of acknowledging their faith and the inherent limitations of what they think they know. For example, I will probably get many down thumbs for this answer largely because some people find it offensive to their preconceptions of the world, whatever side of the fence they sit on. Close-minded bigotry is what stunts intellectual progress in any field.