Let us consider the following metric in $2+1$ dimensions:
$$
\mathrm{d}s^2 = \tilde{g}_{tt} \, \mathrm{d}t^2 + g_{rr} \, \mathrm{d} r^2 + g_{\phi \phi} \,( \mathrm{d} \phi - \omega \, \mathrm{d} t)^2,
$$
where the metric components are functions of $r$ and $\phi$ only. (Note that the metric component $g_{tt} = \tilde{g}_{tt} + \omega^2 g_{\phi \phi}<0$.)
While it is true that two-dimensional hypersurface defined by a constant $t$ will have the same line-element for all $t$, it is not true that the Killing vector $\xi^\mu = (1, 0, 0)$ will be orthogonal to this hypersurface.
Note that when we say some vector is orthogonal to a surface, it means the vector will be orthogonal to all the vectors that are tangent to the surface. The hypersurface of constant $t=t_0$ can be described by the vector equation,
$$
x^\mu = ( t_0, \, r , \, \phi),
$$
where $r$ and $\phi$ parametrise the surface. Let $y_a$ be coordinates on the hypersurface. The natural coordinates on the hypersurface are, of course, $r$ and $\phi$. The set of tangent vectors on the hypersurface are given by,
$$
e^\mu_{(a)} = \frac{\partial x^\mu}{\partial y^a}.
$$
Explicitly, the components of the two tangent vectors are given by,
$$
e^\mu_{(r)} = (0, 1, 0) ,
$$
and
$$
e^\mu_{(\phi)} = (0, 0, 1) .
$$
We will say the Killing vector is orthogonal to the hypersurface if for each $a$,
$$
g_{\mu \nu} \xi^\mu e^\nu_{(a)} = 0.
$$
Note that this condition is satisfied when $a=r$. However, because of the presence of the non-zero off-diagonal component of the metric,
$$
g_{t\phi} = - \omega g_{\phi \phi},
$$
we would have,
$$
g_{\mu \nu} \xi^\mu e^\nu_{(\phi)} = g_{t\phi} = - \omega g_{\phi \phi}.
$$
Thus, when $\omega \neq 0$, the Killing vector is never orthogonal to the hypersurface of constant $t$. If $\omega = 0$, the Killing vector would be hypersurface orthogonal and the spacetime would be static.
Intuitively, a spacetime is static when the line element is invariant under time reversal $t \to - t$, in the usual coordinate system. To make a more precise statement, if a timelike Killing vector field $\xi$ satisfies
$$
\xi_{[\mu} \nabla_\nu \xi_{\rho]} =0,
$$
then it is hypersurface orthogonal and the spacetime is static. See the discussion in section 1.3 of the notes you are referring to. You can also have a look at Wald's GR textbook.