Every finite geometry (projective planes, generalized polygons, polar spaces, near polygons, etc.) and every block design (Witt design, difference sets, Steiner triple systems, etc.) is a hypergraph. So, all the applications of those objects can be considered as applications of hypergraphs.
For example, this paper discusses the application of finite projective planes in coding theory and cryptography: https://www.math.uniri.hr/NATOStorme -ASI/abstracts/storme.pdf Applications of finite geometry in coding theory and cryptography. Inside mathematics, there are many other applications of these hypergraphs in group theory, extremal combinatorics and graph theory.