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You have to delete a 2-dimensional slice. That's what corresponds to a vertex. So the analogous statement for $n$-dimensional arrays will be about arrays in which every $n-1$-dimensional slice has at least one 1.
By the same reasoning the exponential generating function for (labeled) graphs without isolated vertices is $e^{-x}\sum_{n=0}^\infty 2^{\binom n2} x^n/n!$; these correspond to symmetric 0-1 matrices with 0s on the diagonal and a 1 in every row. (oeis.org/A006129)
No, there's nothing special about two dimensions. The analogous statement will be true for 3D arrays. Think of a 3D 0-1 arrays as tricolored 3-regular hypergraph: you have three vertex sets each a different color, corresponding to the three coordinates, and each 1 of the array corresponds to a triple of vertices, one of each color. Each such hypergraph will be a set of isolated vertices together with a hypergraph without isolated vertices.