How to determine proportion of quadratic residues in elliptic curve group?
I have read that the proportion is close to $\frac{1}{2}$


That is, in fact, correct; it is (for large $p$) extremely close to $\frac{1}{2}$; hence if you need your hashing process to fail with probability at most $2^{-64}$, you need your parameter $k \ge 64$


  I would imagine that the proportion of $x \in \mathbb{F}_q$ that do not result in quadratic residues is calculated $\frac{q - n}{q}$, which would be negligible


I believe that's where you're getting confused; you appear to be reasoning "we know there must be $n-1$ solutions to $y^2 = x^3 + ax + b$; there are $q$ possible values of $x$, and as $q \approx n$, then almost every possible value $x$ must be part of a solution.

The part that you're missing is that, for (almost) every value of $x$ which is a solution, there are two possible $y$ values that correspond to it; that is, if the pair $(x,y)$ is a solution to $y^2 = x^3 + ax + b$, then so is $(x, -y)$.  The sole exception to this is if $(x, 0)$ is a solution, there are at most 3 possible $x$ values that satisfy this; as 3 is tiny compared to $q$, we can ignore this for this analysis.

Because of this, there are approximately $(n-1)/2$ possible $x$ values that are possible solutions to the equation; that is, that result in a quadratic residue.  Because $n \approx q$, $(n - 1) / 2 / q \approx \frac{1}{2}$