The asymptotic result I got was $S_n(p,q)\approx ( 4 n \pi p q)^{-1/2}$.
Derivation
Let $f(x)= (q+p e^{ix})$. It has the property that $(f(x))^n= \sum_k c_k e^{i kx}$ where $c_k=C(n,k) q^{n-k} p^k$.
By using the orthogonality relations for these fourier components $e^{i kx}$ one deduces the Parseval formula
$\frac{1}{2\pi} \int_{-\pi}^{\pi} f^n(x) \overline {f^n(x)} dx= \sum_k c_k^2=S_n$. This is the sum of squared binomials you wish to evaluate.
But some trig identities allow us to simplify $f(x)\overline {f(x)}= (1 - 4pq \sin^2(x/2))$.
Thus we seek an asymptotic estimate for the behavior of the exact expression
$$S_n= \frac{1}{2\pi} \int_{-\pi}^{\pi} ( 1- 4p q \sin^2(x/2))^N dx$$
The nonnegative expression $( 1- 4p q \sin^2(x/2))$ has a unique maximum located at $ x=0$ where it peaks at height $1$.
Its minima are at the endpoints of integration, where it takes the value $1-4pq<1$. Note it is roughly bell-shaped. Raising it to high powers preserves these features. The maximum height remains 1, the minimum height drops lower as we increase the powers.
The standard trick is to make a change of variables near the origin so that $ 1- 4p q \sin^2(x/2) =e^{-u^2} $. (Then one can treat this as essentially a Gaussian integral.)
The change of variables is $- u^2 = \ln ( 1- 4p q \sin^2(x/2)) \approx -4p q \sin^2(x/2)$ so $u\approx 2\sqrt{pq} \sin (x/2) \approx \sqrt{pq} x$. That allows us to write $ du \approx \sqrt{pq} dx$
Thus $(1- 4 pq \sin^2(x/2))^n dx =e^{-n u^2} dx \approx \frac{1}{\sqrt{pq}} e^{-n u^2} du$.
Integrating in $u$ we get the result
$$ S_n \approx \frac{1}{2\pi} \frac{1}{\sqrt{pq}} \int e^{- nu^2} du $$
The interval of integration is approximately $|u|< \sqrt{pq}$.
The change if variable $ u= v/\sqrt{n}$ converts the last integral to $\int e^{- n u^2} du =\frac{1}{\sqrt{n}}\int _{|v|\leq \sqrt{npq}|} e^{-v^2} dv =\frac{1}{\sqrt{n}} I_n$
where $I_n\to \int_{-\infty}^{\infty} e^{- v^2} dv = {\sqrt{\pi}}$.
Concluding, $S_n\approx \frac{1}{2 \pi} \frac{\sqrt{pi}}{\sqrt{ npq}} =\frac{1}{\sqrt{4 \pi n pq}}$
P.S. Should you desire more accuracy you can expand the change of variables to higher order as $u= \sqrt{p q } x+\frac{x^3 (6 p q-1) \sqrt{p q }}{24 }+O\left(x^5\right)$.
P.P.S. When $n=16$ and $(p,q)=(.8,.2)$ the approximation was accurate t0 3 decimal places: .1776 exact vs. .1773 approx