Suppose that we selected $m$ random elements of $S_k$. An element $s$ of $S_k$ appears in the induced matrix iff (i) there is a selected element in the row of $s$ in $A$; and (ii) there is a selected element in the column of $s$ in $A$. Call such an element $s$ lucky, and so $X$ is the number of lucky elements.
Under selection without replacement, the probability $P$ of a fixed element $s\in S_k$ to be lucky equals $$P = 1 - \frac{2\binom{Nk-k}{m} - \binom{Nk-(2k-1)}{m}}{\binom{Nk}{m}},$$ where $\binom{Nk-k}{m}/\binom{Nk}{m}$ is the probability that nothing is selected from the row of $s$ in $A$, and $\binom{Nk-(2k-1)}{m}/\binom{Nk}{m}$ is the probability that nothing is selected from neither the row nor the column of $s$ in $A$.
Similarly, under selection with replacement, we have $$P = 1 - \frac{2(Nk-k)^m - (Nk-(2k-1))^m}{Nk^m}.$$$$P = 1 - \frac{2(Nk-k)^m - (Nk-(2k-1))^m}{(Nk)^m}.$$
Then $$E[X](m,N,k) = Nk\cdot P.$$