I believe that the answer is "yes".
I will not assume that $A$ is Noetherian in what follows, but will make
more specific assumptions as necessary, which will hopefully add clarity.
Some preliminary remarks:
One remark is that I don't think it is any loss of generality to assume that $A$ is $\mathfrak a$-adically complete. The reason is that (writing $\hat{A}$ to denote the $\mathfrak a$-adic completion of $A$), if $M$ and $N$ are $\mathfrak a$-adically complete, then the $A$-action on $M$ and $N$ extends canonically to
an $\hat{A}$-action, and any $A$-linear homomorphism between them is necessarily
$\hat{A}$-linear.
If $N$ is $\mathfrak a$-adically separated, then it is clear that
the same is true of $Hom_A(M,N)$ (since if $\varphi \in \mathfrak a^i Hom_A(M,N)$,
then $\varphi(M) \subset \mathfrak a^i N$).
If $M$ is finitely presented (equivalently, finitely generated when $A$ is Noetherian), then applying $Hom_A(M,\text{--})$ to a finite presentation $A^m \to A^n \to M \to 0$ of $M$, we obtain an exact sequence
$$0 \to Hom_A(M,N) \to N^n \to N^m.$$
Thus in this case $Hom_A(M,N)$ is $\mathfrak a$-adically complete,
since it is the kernel of a map between $\mathfrak a$-adically complete
modules.
The main part:
Let $\varphi_i \in \mathfrak a^i Hom_A(M,N)$, for $i \geq 0$. If $m \in M$, then
we find that $\varphi_i(m) \in \mathfrak a^i N,$ and hence that
$\varphi(m):= \sum_{i = 0}^{\infty} \varphi_i(m)$ is well-defined in $N$
(since $N$ is $\mathfrak a$-adically complete). The map $m \mapsto
\varphi(m)$ gives a well-defined homomorphism from $M$ to $N$.
One would like to say that $\varphi$ is the $\mathfrak a$-adic sum of the $\varphi_i$ in
$Hom_A(M,N),$ and hence that $Hom_A(M,N)$ is $\mathfrak a$-adically complete.
However, I don't see how to do this in general. The problem is
that for this, one needs to show that $\sum_{i \geq i_0} \varphi_{i}$ (defined
pointwise, as in the preceding construction) actually lies in
$\mathfrak a^{i_0} Hom_A(M,N)$ (or at least in $\mathfrak a^j Hom_A(M,N)$
for some value of $j$ which goes to $\infty$ as $i_0$ does), and I don't
see how to do this in general. (Each map $\varphi_i$ for $i \geq i_0$ is
in $\mathfrak a^{i_0} Hom_A(M,N)$ by assumption; the problem is to deduce
that $\sum_{i \geq i_0} \varphi_{i}$, which is defined pointwise, is also
in there. This involves effecting some kind of "division by $\mathfrak a^{i_0}$" in $Hom_A(M,N)$, which I don't see how to do in general.)
Suppose now that $\mathfrak a$ is finitely generated (which certainly holds
if $A$ is Noetherian). Then $\mathfrak a^{i_0}$ is finitely generated,
say by elements $a_1,\ldots,a_s$, and so for each $i \geq i_0$, we may
write $\varphi_i = \sum_{j = 1}^s a_j \psi_{i,j}$, where $\psi_{i,j}
\in \mathfrak a^{i-i_0} Hom_A(M,N)$. (Here I am using the fact that
$\varphi_{i} \in \mathfrak a^i Hom_A(M,N) = \sum_{j = 1}^s a_j \mathfrak a^{i-i_0} Hom_A(M,N)$.)
Now we may define $\psi_j := \sum_{i \geq i_0} \psi_{i,j}$ pointwise
as an element of $Hom_A(M,N)$, for $j = 1,\ldots,s$ (again using the fact that $N$ is $\mathfrak a$-adically complete). On the one hand, one easily checks (just
by working pointwise) that $\sum_{j=1}^s a_j \psi_j = \sum_{i \geq i_0}
\varphi_i$. On the other hand, one sees that$\sum_{j = 1}^s a_j \psi_j \in \mathfrak a^{i_0} Hom_A(M,N).$
We conclude that indeed $\sum_{i \geq i_0} \varphi_i$ does lie in
$\mathfrak a^{i_0} Hom_A(M,N),$
and hence that $\varphi$ is the $\mathfrak a$-adic sum of the $\varphi_i$.