Notions of information content and randomness of binary square matrix
You claim that unraveling the (square) matrix into a vector loses some information. However, the transformation is bijective - given the $n^2$ vector, you can easily reconstruct the $n\times n$ matrix. Information theory is oblivious to representation. If you have some random variable $X$ and some bijection defined on its domain $f$ then $H(X) = H(f(X))$. So classical information theory covers the case of matrices.