Actually, the matrix $A$ defines a $q$-ary lattice $L$, but it is not a basis of $L$.
Let $m \ge n$, write $A$ in blocks, as follows: $A = \begin{pmatrix} A_1 \\ A_2 \end{pmatrix}$, where $A_1 \in \mathbb{Z}_q^{n\times n}$ and $A_2 \in \mathbb{Z}_q^{m-n\times n}$. Additionally, let's also write the vectors $x \in L$ as "block" vectors $(x_1 \quad x_2)$.
Now, suppose that $A_1$ is invertible over $\mathbb{Z}_q$.
Then we see that $x \in L \Leftrightarrow x = Az \mod q \Leftrightarrow x_1 = A_1z \mod q \text{ and } x_2 = A_2z \mod q $.
But that means that $A_1^{-1}x_1 = z \mod q$ and $x_2 = A_2(A_1^{-1}x_1) \mod q$.
Therefore, over the integers, there is an $(m-n)$-dimensional vector $u$ such that $x_2 = A_2A_1^{-1}x_1 + qu$.
Thus, it is easy to see that the columns of the following matrix form a basis of $L$:
$$B = \begin{pmatrix} I_n & O \\ A_2A_1^{-1} & qI_{m-n} \end{pmatrix} \in \mathbb{Z}^{m\times m}.$$
If we do $B\begin{pmatrix} x_1 \\ u \end{pmatrix}$ we get exactly $\begin{pmatrix} x_1 \\ A_2A_1^{-1}x_1 + qu \end{pmatrix}$, as expected.
Now, answering your other questions:
Do these also have the same kind of parallelogram structure?
Yes, all lattices have such structure. The parallelogram in this case is defined by the columns of $B$.
Why do cryptographers use these lattices?
Those lattices appear naturally in cryptography because of problems like SIS and LWE.
There is plenty of material about that on the internet, for example, this tutorial on lattice-based crypto.