Rewritten and (I hope) clarified
Yes, every subgroup can be characterized as the set of tuples satisfying certain linear congruences in its entries. To be more precise, we have the following:
Let $p$ be a prime. Then every subgroup of $\displaystyle \prod_{i=1}^n \mathbb{Z}_{p^k}$ (including the subgroups of a $G$ as given in the statement of the question) can be described as the set of elements $(h_1,\ldots,h_n)$ which satisfy a set of (at most) $n$ congruences of the following form: $\begin{align*} h_{\sigma(1)} &\equiv 0 \pmod{p^{j_1}}\\ h_{\sigma(2)} &\equiv \alpha_{21}h_{\sigma(1)} \pmod{p^{j_2}}\\ h_{\sigma(3)} &\equiv \alpha_{31}h_{\sigma(1)} + \alpha_{32}h_{\sigma(2)} \pmod{p^{j_3}}\\ &\vdots\\ h_{\sigma(n)} &\equiv \alpha_{n1}h_{\sigma(1)} + \alpha_{n2}h_{\sigma(2)} + \cdots + \alpha_{n(n-1)}h_{\sigma(n-1)} \pmod{p^{j_n}} \end{align*}$ where $\sigma\in S_n$ is a permutation of $\{1,\ldots,n\}$, $0\leq j_1\leq\cdots\leq j_n\leq k$ are nonnegative integers, and $\alpha_{ij}$ are integers.
What follows is essentially the proof that submodules of free modules over PIDs are free, as described in this previous answer, particularized for this situation.
Let $H$ be a subgroup of $\displaystyle \prod_{i=1}^n \mathbb{Z}_{p^k}$.
We proceed by induction on $n$. If $n=1$, then $H$ is a subgroup of $\mathbb{Z}_{p^k}$, and therefore is of the form $p^{j_1}\mathbb{Z}_{p^k}$ for some $j_1$, $0\leq j_1 \leq k$; thus, $(h_1)\in H$ if and only if $h_1\equiv 0\pmod{p^{j_1}}$, which gives the result we want.
Asume the result holds for subgroups of a product of $n$ copies of $\mathbb{Z}_{p^k}$, and let $H$ be a subgroup of $\displaystyle \prod_{i=1}^{n+1}\mathbb{Z}_{p^k}$.
If $H=\{e\}$, then we are done: $H$ is described by the congruences $h_i\equiv 0\pmod{p^{k}}$, $i=1,\ldots,n$. So we may assume $H$ is nontrivial.
Consider the projections onto the $n+1$ coordinates; if any projection, say the projection on the $j$th component is trivial, then $H$ is a subgroup of a product of $n$ copies of $\mathbb{Z}_{p^k}$, and can be described as in the proposition, together with the condition $h_j\equiv 0\pmod{p^k}$.
Assume then that all projections are nontrivial. Each projection gives a subgroup of $\mathbb{Z}_{p^k}$, hence of the form $p^{r_i}\mathbb{Z}_{p^k}$, with $0\leq r_i\lt k$. Let $\sigma(1)$ be the index with the largest subgroup (i.e., smallest $r_i$, possibly $0$); set $j_1 = r_{\sigma(1)}$. Let $\mathbf{a}_1$ be an element of $H$ whose $\sigma(1)$ coordinate is $p^{j_1}$. The minimality of $j_1$ means that $\mathbf{a}_{1}$ can be written as $\mathbf{a}_1 = (a_1,\ldots,a_n) = p^{j_1}(b_1,\ldots,b_n) = a_{\sigma(1)}(b_1,\ldots,b_n)$ with $b_{\sigma(1)}=1$, all $b_i$ integers.
Now let $K$ be the subgroup of $H$ corresponding to the kernel of the projection onto the $\sigma(1)$-coordinate; that is, all elements that have $\sigma(1)$ coordinate congruent to $0$ modulo $p^{k}$. By induction, there is a bijection $\sigma\colon \{2,\ldots,n+1\}\to\{1,\ldots,n+1\}-\{\sigma(1)\}$ and integers $\gamma_{rs}$, $2\leq r\leq n+1$, $1\leq s\lt r$ and nonnegative integers $j_2\leq\cdots\leq j_{n+1}\leq k$ such that the elements of $K$ can be described as $\begin{align*} k_{\sigma(1)} &\equiv 0 \pmod{p^k}\\ k_{\sigma(2)} &\equiv 0 \pmod{p^{j_2}}\\ k_{\sigma(3)} &\equiv \gamma_{32}k_{\sigma(2)} \pmod{p^{j_3}}\\ &\vdots\\ k_{\sigma(n+1)} &\equiv \gamma_{(n+1)2}k_{\sigma(2)} + \cdots + \gamma_{(n+1)n}k_{\sigma(n)}\pmod{p^{j_{n+1}}}. \end{align*}$ Moreover, the minimality of $j_1$ ensures that $j_1\leq j_2$.
Now, $K\cap\langle \mathbf{a}_1\rangle = \{e\}$, and $K+\langle \mathbf{a}_1\rangle\subseteq H$. In fact, $H = K\oplus\langle\mathbf{a}_1\rangle$: given $\mathbf{h}\in H$, we know that the $\sigma(1)$-component of $\mathbf{h}$ is a multiple of $p^{j_1}$ (by choice of $\sigma(1)$), and so there exists $m$ such that $\mathbf{h}- m\mathbf{a}_1 \in K$. Hence, $h\in K\oplus\langle\mathbf{a}_1\rangle$.
Therefore, given $\mathbf{h}=(h_1,\ldots,h_{n+1})\in \displaystyle\prod_{i=1}^{n+1}\mathbb{Z}_{p^k}$, we have that $\mathbf{h}\in H$ if and only if:
- (i) $h_{\sigma(1)}\equiv 0\pmod{p^{j_1}}$; and
- (ii) if $h_{\sigma(1)} = mp^{j_1}$, then $\mathbf{h}-m\mathbf{a}_1\in K$.
Thus, we only need to show that this can be expressed by congruences of the form described. Note that $h_{\sigma(1)} = ma_{\sigma(1)} = mp^{j_1}$.
Condition (i) on $\mathbf{h}$ can be written as $h_{\sigma(1)} \equiv 0 \pmod{p^{j_1}}.$ By our prior description of $K$, condition (ii) can be described as: $\begin{align*} h_{\sigma(2)} -ma_{\sigma(2)}&\equiv 0 \pmod{p^{j_2}}\\ h_{\sigma(3)} -ma_{\sigma(3)}&\equiv \gamma_{32}\bigl(h_{\sigma(2)}-ma_{\sigma(2)}\bigr) \pmod{p^{j_3}}\\ &\vdots\\ h_{\sigma(n+1)}-ma_{\sigma(n+1)} &\equiv \gamma_{(n+1)2}\bigl(h_{\sigma(2)}-ma_{\sigma(2)}\bigr) + \cdots + \gamma_{(n+1)n}\bigl(h_{\sigma(n)}-ma_{\sigma(n)}\bigr)\pmod{p^{j_{n+1}}} \end{align*}$ with the problem that $m$ depends on $h_{\sigma(1)}$.
However, $a_{\sigma(i)} = p^{j_1}b_{\sigma(i)} = a_{\sigma(1)}b_{\sigma(i)}$, and since $ma_{\sigma(1)} \equiv h_{\sigma(1)} \pmod{p^{k}}$ then for each $i$, $2\leq i\leq n+1$ we have $ma_{\sigma(i)} = ma_{\sigma(1)}b_{\sigma(i)} \equiv h_{\sigma(1)}b_{\sigma(i)}\pmod{p^{k}}.$ Since $j_i\leq k$, we can then rewrite the congruences above as: $\begin{align*} h_{\sigma(1)} &\equiv 0 \pmod{p^{j_1}}\\ h_{\sigma(2)} -h_{\sigma(1)}b_{\sigma(2)}&\equiv 0 \pmod{p^{j_2}}\\ h_{\sigma(3)} -h_{\sigma(1)}b_{\sigma(3)} &\equiv \gamma_{32}\bigl(h_{\sigma(2)}-h_{\sigma(1)}b_{\sigma(2)}\bigr) \pmod{p^{j_3}}\\ &\vdots\\ h_{\sigma(n+1)}-h_{\sigma(1)}b_{\sigma(n+1)} &\equiv \gamma_{(n+1)2}\bigl(h_{\sigma(2)}-h_{\sigma(1)}b_{\sigma(2)}\bigr) \\ &\qquad\qquad\mathop{+} \cdots \mathop{+} \gamma_{(n+1)n}\bigl(h_{\sigma(n)}-h_{\sigma(1)}b_{\sigma(n)}\bigr)\pmod{p^{j_{n+1}}} \end{align*}$ which can be rewritten in the desired form by moving the $h_{\sigma(1)}b_{\sigma(k)}$ summand to the right hand side, and regrouping; this satisfies the conditions of the statement above, since $b_1,\ldots,b_n$ and $\gamma_{ij}$ are fixed, giving rise to fixed $\alpha_{ij}$ that do not depend on $\mathbf{h}$.
This establishes the induction step, and so the description.