Yes. But there are some things to discuss first to help you understand.
When discussing a "linear mapping" one typically requires that it be defined on a full linear space, not some convex subset. For now, let $B(H)$ denote the linear space of all bounded linear operators on $H$, then $S(H)$ is a convex subset of $B(H)$.
Now we can use linearity of $M$ to allow for the equality $M(\alpha X + \beta Y) = \alpha M(X) + \beta M(Y)$ to hold for arbitrary operators $X$ and $Y$ and arbitrary complex numbers $\alpha$ and $\beta$ (i.e., not just for density operators).
Because $M$ and $N$ agree on all product density operators, by linearity of $M$ and $N$ they must agree on all product operators as well. That is, it must be the case that $$M(X\otimes Y) = N(X\otimes Y)$$ holds for all $X\in B(H_A)$ and $Y\in B(H_B)$.
If $H_A$ and $H_B$ are finite-dimensional Hilbert spaces, then $B(H_A)$, $B(H_B)$ and $B(H_A\otimes H_B)$ are all finite dimensional as vector spaces as well, where we note that $$B(H_A\otimes H_B)\simeq B(H_A)\otimes B(H_B).$$
In this case, the tensor product operator space $B(H_A\otimes H_B)$ is spanned by the product operators,
$$
B(H_A\otimes H_B) = \operatorname{span}\big(\big\{X\otimes Y\, :\, X\in B(H_A), Y\in B(H_B)\big\}\big),
$$
and so $M$ and $N$ must agree on the whole space.
If they are infinite dimensional, then equality of $M$ and $N$ follows from the universal property of tensor product spaces. See this answer.