It seems to me is that there are a lot of things in mathematics that one could call hypermatrices if one were so inclined, but which people generally don't (and if they call them anything, they call them tensors). For example, one use of matrices $M$ is that they represent bilinear forms $x^T M y$ and quadratic forms $x^T M x$. Three-dimensional hypermatrices then represent trilinear forms and cubic forms (and so forth for higher dimensions), and these do appear in various places in mathematics, for example in Lie theory. The norm map on a cubic number field is also an example of a cubic form. More generally, alternating multilinear forms appear as differential forms, and the same can be said about more general types of tensors. It could be said that studying a projective hypersurface defined by a homogeneous polynomial $f(x_1, ... x_n) = 0$ is the same as studying a certain $n$-dimensional hypermatrix associated to $f$. It could be said that studying a finite-dimensional algebra or Lie algebra $A$ is the same as studying the hypermatrix giving the structure constants of its multiplication or bracket $m : A \times A \to A$.
So, as I said in the comments, I'm not sure what you mean when you say that hypermatrices are rare. I suppose you are trying to draw a distinction between basis-dependent and basis-independent ideas?
