What follows is really a heuristic rather than rigorous proof, but hopefully provides some intuition.
Consider first the case where $q$ is fixed and is given to be $q_0 = (1/2,1/2)$, so is in the middle of the box. For a fixed radius $r > 0$ let $D_r^{(q_0)} = \left\{x \, \colon \, |x-q_0| < r\right\}$ denote the disk of radius $r$, and define
$$N_r^{(q_0)} = \# \left\{ x_i \, \colon \, x_i \in D_r^{(q_0)}\right\},$$
the number of the (random) points that fall inside the disk. The probability that any given point is inside the disk is equal to
$$\mathbf P[ x_i \in D_r] = \frac{ \text{Area}( D_r \cap [0,1]^2 )}{\text{Area}([0,1]^2)}$$
for small enough values of $r$, $D_r \subset [0,1]^2$, and the formula above becomes
$$ \mathbf P[x_i \in D_r] = \pi r^2.$$
In particular it follows that for sufficiently small $r$, $N_r^{(q_0)}$ follows a binomial distribution with success probability $\pi r^2$. This is well defined so long as $r < 1/\sqrt{\pi}$.
Now we turn to the random variable you were interested in (with the caveat that we have fixed $q$), which we denote $M_n^{(q)}$
$$M_n^{(q_0)} = \min_{i = 1,\ldots,n} \{|x_i - q|\}$$
We can relate this to the random variable $N_r^{(q)}$ by the formula
$$
\mathbf P[ M_n^{(q_0)} \leq r] = \mathbf P[ N_r^{(q_0)} > 0]$$
That is: there is a point within a distance $r$ of $q_0$ (i.e. $M_n^{(q_0)} \leq r$), if and only if there is at least one point inside the disk $D_r^{(q_0)}$, which is to say $N_r^{(q_0)} > 0$.
So (under the assumption that $r$ is small) we have
$$
\begin{aligned}
\mathbf P[ M_n^{(q_0)} \leq r] &= \mathbf P[\text{Bin}(n, \pi r^2) > 0] \\
& = 1 - (1-\pi r^2)^n
\end{aligned}
$$
That is, we have the CDF for the variable $M_n^{(q_0)}$, from which we can derive the PDF by differentiation
$$
\begin{aligned}
f_n^{(q_0)}(r)& = \frac{d}{dr}\mathbf P[ M_n^{(q_0)} \leq r] \\
&= 2 \pi n r(1 - \pi r^2)^{n-1}
\end{aligned}
$$
which we define on the range $[0, 1/\sqrt{\pi}]$. Then we can calculate the expected value
$$
\mathbf E[M_n^{(q_0)}] = \int_0^{1/\sqrt{\pi}} r f_n^{(q)}(r)dr = \frac{n}{2} \frac{\Gamma(n)}{\Gamma(n+3/2)}$$
(I admit, that I used wolframalpha to derive this. We can now evaluate the Taylor series at infinity to get the asymptotic formula for this, which indeed is $O(n^{-\frac12})$, (again, I had to rely on wolframalpha for this).
So we have a heuristic for why given a fixed $q$ away from the boundary of the box we might expect the minimum distance to be of the order $n^{-\frac12}$.
Extending this to the case where $q$ is not fixed is now quite (heuristicallly!) simple by conditioning on q:
$$
\begin{aligned}
\mathbf E[ M_n] & = \int_{[0,1]^2} \mathbf E[ M_n^{(\rho)} ] \mathbf P[q = \rho] d \rho \\
& = \int_{[0,1]^2} \mathbf E[ M_n^{(\rho)} ]d\rho
\end{aligned}
$$
For points $\rho$ away from the boundary, this expectation is independent of $\rho$, and since the vast majority of points are away from the boundary we have
$$
\begin{aligned}
\mathbf E[ M_n] &\sim \int_{[0,1]^2} \mathbf E[ M_n^{(q_0)} ]d\rho \\
& = \mathbf E[ M_n^{(q_0)} ] \\
& = \frac{n}{2} \frac{\Gamma(n)}{\Gamma(n+3/2)}
\end{aligned}
$$
Again, this is all very heuristic, but hopefully gives you some intuition!