Firstly, $\vec{Q}$ is not an arbitrary vector. It's right there in your question: $\vec{\eta} = S\vec{Q}$, or equivalently, $\vec{Q} = S^{-1}\vec{\eta}$. This is a physical problem - for a given initial condition, only one thing happens, and that one unique thing is represented mathematically by the vector $\vec{\eta}(t)$. The transformation lets you simply change the coordinates to write your equations of motion more simply, as two separate equations for $Q_1$ and $Q_2$ instead of all the components of $\vec{\eta}$ mixed together.
Now, when you perform the transformation $W_D = S^{-1}WS$, you should be using an orthogonal transformation matrix (so that $S^{-1} = S^T$). When you use an orthogonal transformation matrix, the eigenvalues of $W_D$ are the same as the eigenvalues of $W$! In fact, finding the eigenvalues and eigenvectors of $W$ is an integral part of calculating the transformation matrices!
Let's say $W$ has two eigenvalues, $\omega_1^2$ and $\omega_2^2$, with corresponding eigenvectors $\vec{v}_1 = [v_{11}\hspace{1ex}v_{12}]$ and $\vec{v}_2 = [v_{21}\hspace{1ex}v_{22}]$ (so $W\vec{v}_1 = \omega_1^2\vec{v}_1$ and $W\vec{v}_1 = \omega_1^2\vec{v}_1$). We should also make sure that $\vec{v}_1$ and $\vec{v}_2$ are both unit vectors - both should have a magnitude of 1.
It's also safe to assume $W$ is Hermitian (such matrices in physics always are. For a real-valued matrix, like here, that means $W$ is symmetric. The coupling between 1 and 2 is the same as between 2 and 1). This means $\vec{v}_1$ and $\vec{v}_2$ have the nice property that $\vec{v}_1\cdot\vec{v}_2 = 0$.
So now, if we construct a matrix $S$ like this:
$$S = [\vec{v}_1 | \vec{v}_2] = \begin{bmatrix}v_{11} & v_{21} \\ v_{12} & v_{22}\end{bmatrix}$$
notice what happens: the first column of $WS$ will be $W\vec{v}_1$, which is just $\omega_1^2\vec{v}_1$. The second column will similarly be $\omega_2^2\vec{v}_2$. So:
$$WS = [\omega_1^2\vec{v}_1 | \omega_2^2\vec{v}_2] = \begin{bmatrix}\omega_1^2v_{11} & \omega_2^2v_{21} \\ \omega_1^2v_{12} & \omega_2^2v_{22}\end{bmatrix}$$
(if you don't believe me you should try it yourself. It has to do with how eigenvectors are defined - this is their whole thing)
Now, let's multiply this whole thing by $S^T$:
$$S^T = \left[\frac{\vec{v}_1}{\vec{v}_2}\right] = \begin{bmatrix}v_{11} & v_{12} \\ v_{21} & v_{22}\end{bmatrix}$$
and compute $S^TWS$. But notice what happens when we do so: when we multiply the first row by the first column, we're really taking the dot product of $\vec{v}_1$ and $\omega_1^2\vec{v}_1$. When we multiply the first row and the second column, we are really taking the dot product $\vec{v}_1\cdot\omega_2^2\vec{v}_2$. In all:
$$S^TWS = \begin{bmatrix}
\omega_1^2(\vec{v}_1\cdot\vec{v}_2) & \omega_2^2(\vec{v}_1\cdot\vec{v}_2) \\
\omega_1^2(\vec{v}_2\cdot\vec{v}_1) & \omega_2^2(\vec{v}_2\cdot\vec{v}_2)
\end{bmatrix}$$
BUT remember: $\vec{v}_1$ and $\vec{v}_2$ are unit vectors, so $\vec{v}_1\cdot\vec{v}_1 = \vec{v}_2\cdot\vec{v}_2 = 1$, and we also saw that $\vec{v}_1\cdot\vec{v}_2 = \vec{v}_2\cdot\vec{v}_1 = 0$ because $W$ is symmetric. So:
$$S^TWS = \begin{bmatrix}
\omega_1^2 & 0 \\
0 & \omega_2^2
\end{bmatrix} = W_D$$
And voila! Diagonalized! We can immediately see that $W_D$ has eigenvectors $[1\hspace{1ex}0]$ and $[0\hspace{1ex}1]$, with corresponding eigenvalues $\omega_1^2$ and $\omega_2^2$, the same as the eigenvalues of $W$, just on a new basis.
Now here's the kicker.
We take the original equation of motion:
$$\ddot{\vec{\eta}} = -W\vec{\eta}$$
and multiply both sides by $S^T$:
$$S^T\ddot{\vec{\eta}} = -S^TW\vec{\eta}$$
We can also sneak in $SS^T$ in between $W$ and $\vec{\eta}$ on the right hand side, because $SS^T = SS^{-1}$ is just the identity matrix:
$$S^T\ddot{\vec{\eta}} = -S^TWSS^T\vec{\eta}$$
Inserting some parentheses:
$$S^T\ddot{\vec{\eta}} = -(S^TWS)(S^T\vec{\eta})$$
and we recover (given $\vec{Q} = S^T\vec{\eta}$):
$$\ddot{\vec{Q}} = -W_D\vec{Q}$$
which of course decouples into
$$\ddot{Q}_1 = -\omega_1^2 Q_1$$
and
$$\ddot{Q}_2 = -\omega_2^2 Q_2$$
So the solutions $Q_{1,2}$ are oscillators with frequencies $\omega_{1,2}^2$ because $\omega_{1,2}^2$ are the eigenvalues of $W$ (and $W_D$). The transformation doesn't change the eigenvalues of your matrix, it only mixes up your coordinates so that the math is easier to deal with.