The separability of $H$ has little influence, the only difference between the separable and the non-separable case is that in the non-separable case, $V^\perp$ has an uncountable Hilbert basis (of the same cardinality as any Hilbert basis of $H$, naturally). Some authors prefer to only treat countable Hilbert bases and therefore restrict to the separable case.
To see that, we look at the spectral theorem for compact operators on Banach spaces, as it is formulated as theorem 4.25 in Rudin's Functional Analysis.
Suppose $X$ is a Banach space, $T \in \mathscr{B}(X)$, and $T$ is compact.
If $\lambda \neq 0$, then the four numbers \begin{align} \alpha &= \dim \mathscr{N}(T - \lambda I)\\ \beta &= \dim X/\mathscr{R}(T - \lambda I)\\ \alpha^\ast &= \dim \mathscr{N}(T^\ast - \lambda I)\\ \beta^\ast &= \dim X^\ast/\mathscr{R}(T^\ast - \lambda I)\end{align} are equal and finite.
If $\lambda \neq 0$ and $\lambda \in \sigma(T)$, then $\lambda$ is an eigenvalue of $T$ and of $T^\ast$.
$\sigma(T)$ is compact, at most countable, and has at most one limit point, namely, $0$.
Nothing in that requires separability, or reflexivity, or that the space is a Hilbert space.
In our case, where we have a self-adjoint compact operator $A\colon H \to H$, we know that the eigenspaces to the eigenvalues $\lambda \neq 0$ are mutually orthogonal, so choosing an orthonormal basis for each such eigenspace, we obtain a countable (finite or countably infinite) orthonormal set $\{ e_i : i \in I\}$ consisting of eigenvectors of $A$. Letting $V = \overline{\operatorname{span}}\: \{ e_i : i \in I\}$, by self-adjointness we have $A(V^\perp) \subset V^\perp$, and the restriction $B \colon V^\perp \to V^\perp$ of $A$ is a self-adjoint compact operator with $\sigma(B) = \{0\}$. It follows that $B = 0$, and hence $V^\perp = \ker A$. Then by extending $\{ e_i : i \in I\}$ by a Hilbert basis $\{ \nu_\kappa : \kappa \in K\}$ of $V^\perp$, we obtain a Hilbert basis of $H$ consisting of eigenvectors of $A$. The obtained Hilbert basis is countable if and only if $H$ is separable.