The Seidel energy is defined as the sum of the absolute values of the eigenvalues of the Seidel matrix of a hypergraph. We first characterize the k-uniform hypergraphs of fixed order n with minimum and maximum Frobenius norms of Seidel matrices and then derive bounds for the Seidel energy. Building on these results, we obtain a negative answer to the hypergraph analogue of Haemers Conjecture by showing that the complete k-uniform hypergraph does not, in general, minimize Seidel energy. Motivated by the theory of hypoenergetic and non-hypoenergetic graphs, we define Seidel hypoenergetic and Seidel non-hypoenergetic hypergraphs and prove that almost all k-uniform hypergraphs are Seidel non-hypoenergetic.