Consider a separable compact Hausdorff space $X$ with $|X| \leq 2^{\aleph_{0}}$.
If $A\subseteq X$ is a closed set with empty interior, must $A$ be separable?
Each example I've been able to come up with in this setting is either countable or can be proven to be separable.
EDIT: Edited question to reflect the question at base.
Here is a counterexample in ZFC. Let $X\subset\{0,1\}^\mathbb{R}$ be the set of characteristic functions of (possibly degenerate or empty) intervals. Then $X$ is closed in $\{0,1\}^\mathbb{R}$ (if $f\in \{0,1\}^\mathbb{R}\setminus X$ then this is witnessed by points $x<y<z$ such that $f(x)=f(z)=1$ and $f(y)=0$ so the complement is open) so $X$ is compact. Also, $X$ is separable, since the characteristic functions of intervals with rational endpoints are dense in $X$, and clearly $|X|=2^{\aleph_0}$.
Now let $A\subset X$ be the set of characteristic functions of sets with at most one element. It is easy to see that $A$ is closed in $X$ and has empty interior. However, $A$ is not separable. Indeed, $A$ is the 1-point compactification of a discrete space of cardinality $2^{\aleph_0}$ (the characteristic functions of singletons form a discrete space, and the zero function is the point at infinity).
Here is another closely related example. Let $Y=[0,1]\times \{0,1\}$ with the lexicographic order and let $X=Y\times Y$. Let $D\subset X$ be the set of points of the form $((x,0),(x,1))$. Then $D$ is discrete, since $(-\infty,(x,1))\times((x,0),\infty)$ isolates $((x,0),(x,1))$ in $D$. So the closure $A$ of $D$ is not separable, but can easily be seen to have empty interior.
(To see how this is related to the first example, identify $((x,i),(y,j))$ with the interval from $x$ to $y$ in $\mathbb R$ where the second coordinates $i$ and $j$ determine whether the endpoints are included.)