A generalization of this integral is $$\small \int_{0}^{\pi} \ln \left(1-2 e^{- \phi} \cos (mx) + e^{- 2\phi} \right) \ln \left( 1-2 e^{- \lambda} \cos(nx) +e^{-2 \lambda}\right) \, \mathrm dx= \frac{2\pi \gcd^{2} (m,n) \operatorname{Li}_{2} \left(\exp \left(- \, \frac{m\lambda +n \phi}{\gcd(m,n)} \right) \right)}{mn} , $$ where $\operatorname{Li}_{2}(-)$ is the dillogarithm, $m$ and $n$ are positive integers, and $\phi, \lambda \ge 0$.
To prove this result, we'll use the Fourier series $$\sum_{n=1}^{\infty} \frac{e^{- k \phi} \cos(k \theta)}{k} = - \frac{1}{2} \, \ln \left(1-2 e^{- \phi} \cos(\theta) +e^{- 2 \phi} \right),$$ which can be derived by extracting the real part of the identity $$\sum_{k=1}^{\infty} \frac{\left(e^{-\phi}e^{i \theta}\right)^{k}}{k} = - \ln \left(1-e^{- \phi} e^{i \theta} \right). $$
We get
$$ \begin{align} &\int_{0}^{\pi} \ln \left(1-2 e^{- \phi} \cos (mx) + e^{- 2\phi} \right) \ln \left( 1-2 e^{- \lambda} \cos(nx) +e^{-2 \lambda}\right) \, \mathrm dx \\&= 4 \int_{0}^{\pi} \sum_{j=1}^{\infty}\frac{e^{- j \phi}\cos(jm x)}{j} \sum_{k=1}^{\infty} \frac{e^{-k \lambda }\cos(kn x)}{k} \mathrm d x \\ &= 4 \sum_{j=1}^{\infty} \sum_{k=1}^{\infty} \frac{e^{- j \phi} e^{- k \lambda}}{jk} \int_{0}^{\pi} \cos(j m x) \cos(kn x) \, \mathrm d x \\ &= 2 \pi \sum_{j=1}^{\infty} \sum_{k=1}^{\infty} \frac{e^{- j \phi} e^{- k \lambda}}{jk} \, \delta_{jm, kn} \\ &= 2 \pi \sum_{p=1}^{\infty} \frac{mn }{p \operatorname{lcm}(m,n) p \operatorname{lcm}(m,n)} \, \exp \left(-\frac{p \operatorname{lcm}(m,n)}{m} \phi
- \frac{p\operatorname{lcm}(m,n)}{n} \lambda \right) \\ &= \frac{2 \pi \gcd^{2}(m,n)}{mn} \, \sum_{p=1}^{\infty} \frac{1}{p^{2}} \, \exp \left(- p \, \frac{m\lambda +n \phi }{\gcd(m,n)} \right) \\ &= \frac{2 \pi \gcd^{2}(m,n)}{mn} \, \operatorname{Li}_{2} \left(\exp \left(- \, \frac{m \lambda+n \phi}{\gcd(m,n)} \right) \right). \end{align}$$
When the value of the integral is very small, Wolfram Alpha sometimes incorrectly says that the value of the integral is zero.
For $\phi=0$ and $\lambda =0$, we have $$ \begin{align} &\int_{0}^{\pi} \ln \left(2-2 \cos(mx) \right) \ln \left(2-2 \cos(nx)\right) \, \mathrm dx \\ &= \int_{0}^{\pi} \ln \left(4 \ \frac{1-\cos(mx)}{2} \right) \ln \left(4 \ \frac{1+ \cos(nx)}{2} \right) \, \mathrm dx \\ &= \small \pi \ln^{2}(4) + \ln(4) \left( \int_{0}^{\pi} \ln\left(\frac{1- \cos(mx)}{2} \right) \, \mathrm dx + \int_{0}^{\pi} \ln \left(\frac{1- \cos(nx)}{2} \right) \, \mathrm dx \right) \\ &+ \small \int_{0}^{\pi} \ln \left(\frac{1- \cos(mx)}{2} \right) \ln \left(\frac{1-\cos(nx)}{2} \right) \, \mathrm dx \\ &\overset{(1)}{=} \small \pi \ln^{2}(4) + \ln(4) \left(-2 \pi \ln(2) -2 \pi \ln(2) \right)+ 2 \int_{0}^{\pi/2} \ln \left(\frac{1- \cos(2mt)}{2} \right) \ln \left(\frac{1-\cos(2nt)}{2} \right) \, \mathrm dt \\&= \color{red}{-4 \pi \ln^{2}(2) +8 \int_{0}^{\pi/2} \ln |\sin(mt)| \ln |\sin(nt) | \, \mathrm dt} \\ & = \frac{2 \pi \gcd^{2}(m,n)}{mn} \, \operatorname{Li}_{2} (1) \\ &= \frac{2 \pi \gcd^{2}(m,n)}{mn} \, \zeta(2) \\ &= \frac{\pi^{3}}{3} \frac{\gcd^{2}(m,n)}{mn}. \end{align}$$
$(1)$
For an positive integer $m$, $$ \begin{align} \int_{0}^{\pi} \ln \left(\frac{1-\cos(mx)}{2} \right) \, \mathrm dx &= \frac{1}{m} \int_{0}^{m \pi} \ln \left(\frac{1-\cos(u)}{2} \right) \, \mathrm du \\ &= \frac{1}{m} \sum_{k=0}^{m-1} \int_{k \pi}^{(k+1) \pi} \ln \left(\frac{1-\cos(u)}{2} \right) \, \mathrm du \\ &= \frac{1}{m} \sum_{k=0}^{m-1} \int_{0}^{\pi} \ln \left(\frac{1 -(-1)^{k} \cos(v)}{2} \right) \, \mathrm dv \\ &= \frac{1}{m} \sum_{k=0}^{m-1} \int_{0}^{\pi} \ln \left(\frac{1 - \cos(v)}{2} \right) \, \mathrm dv \\ &= \int_{0}^{\pi} \ln \left(\frac{1 - \cos(v)}{2} \right) \, \mathrm dv \\ &= \int_{0}^{\pi } \ln \left(\sin^{2}\left(\frac{u}{2}\right) \right) \, \mathrm dv \\ &= 4 \int_{0}^{\pi/2} \ln \left(\sin (v) \right) \, \mathrm dv \\ &= -2 \pi \ln(2) . \end{align}$$
I was going to use $|r| \le 1$ and $|s| \le 1$ instead of $e^{- \theta}$ and $e^{- \lambda}$, but I chose the later because it looked cleaner.