UPDATE: I added a proof showing that $$\int_{0}^{\infty} \left(2J_{0}(2x)^{2} -J_{0}(x)^2 \right) \, \mathrm dx= \int_{0}^{\infty} \left(2Y_{0}(2x)^2 - Y_{0}(x)^{2} \right) \, \mathrm dx. $$
We can use Ramanujan's master theorem to show that $$\int_{0}^{\infty}\left(2J_0(2x)^2-J_0(x)^2\right)\, \mathrm dx = \frac{\ln 2}{\pi}. $$
As $x \to \infty$, $$\left(2J_0(2x)^2-J_0(x)^2\right) \sim \frac{\sin (4x)-\sin (2x)}{\pi x}. $$ So the integral converges conditionally but not absolutely.
The hypergeometric representation of the square of the Bessel function of the first kind of order zero is $$J_{0}(z)^{2} = \, _1F_2\left(\frac{1}{2}; 1, 1; -z^{2} \right). $$
So for $a>0$ and $0 < s < 1$, the Mellin transform of $J_{0}(ax)^{2}$ is $$ \begin{align} \int_{0}^{\infty} x^{s-1} J_{0}(ax)^{2} \, \mathrm dx &= \int_{0}^{\infty} x^{s-1} \, _1F_2\left(\frac{1}{2}; 1, 1; -(ax)^{2} \right) \, \mathrm dx \\ &= \frac{1}{2a^{s}}\int_{0}^{\infty} u^{s/2-1} \, _1F_2\left(\frac{1}{2}; 1, 1; -u \right) \, \mathrm du \\ &= \frac{1}{2a^{s}} \Gamma\left(\frac{s}{2} \right) \frac{\Gamma \left(\frac{1}{2}-\frac{s}{2} \right) \Gamma(1)^{2} }{\Gamma\left(\frac{1}{2}\right) \Gamma\left(1- \frac{s}{2} \right)^{2}} \\ &= \frac{1}{2a^{s}} \Gamma\left(\frac{s}{2} \right) \frac{\Gamma \left(\frac{1}{2}-\frac{s}{2} \right)}{\sqrt{\pi} \, \Gamma\left(1- \frac{s}{2} \right)^{2}} . \end{align}$$
Since $ \int_{0}^{\infty}\left(2J_0(2x)^2-J_0(x)^2\right)\, \mathrm dx $ converges, a property of the Mellin transform allows us to conclude that $$ \begin{align} \lim_{s \to 1^{-}} \int_{0}^{\infty} x^{s-1} \left(2J_0(2x)^2-J_0(x)^2\right)\, \mathrm dx &= \int_{0}^{\infty} \left(2J_0(2x)^2-J_0(x)^2\right)\, \mathrm dx \\ &= \frac{1}{\pi} \lim_{s \to 1^{-}} \left(\frac{1}{2^{s}}- \frac{1}{2} \right) \Gamma \left(\frac{1}{2} - \frac{s}{2} \right) \\ &= \frac{1}{\pi} \lim_{s \to 0^{-}} \left( \frac{1}{2^{s+1}} - \frac{1}{2} \right)\Gamma \left(- \frac{s}{2} \right) \\ &= \frac{1}{\pi} \lim_{s \to 0^{-}} \left(- \frac{\ln 2}{2} s + \mathcal{O}(s^{2}) \right) \left(- \frac{2}{s} + \mathcal{O}(1) \right) \\ &= \frac{\ln 2}{\pi}. \end{align}$$
Let $H_{0}^{(1)}(z) $ be the Hankel function of the first kind of order zero defined as $$H_{0}^{(1)}(z) = J_{0}(z)+iY_{0}(z). $$
To show that $$\int_{0}^{\infty}\left(2J_0(2x)^2-J_0(x)^2\right)\, \mathrm dx$$ and $$\int_{0}^{\infty}\left(2Y_0(2x)^2-Y_0(x)^2\right)\, \mathrm dx $$ have the same value, we can integrate the function $$2\left( H_{0}^{(1)}(2z)\right)^{2}-\left(H_{0}^{(1)}(z) \right)^{2}$$ around a closed, semicircular contour in the upper half-plane that is indented at the origin.
Applying Jordan's lemma, we get $$\int_{0}^{\infty} \left( 2\left( H_{0}^{(1)}(2xe^{i \pi})\right)^{2}-\left(H_{0}^{(1)}(xe^{i \pi} ) \right)^{2} + 2\left( H_{0}^{(1)}(2x)\right)^{2}-\left(H_{0}^{(1)}(x) \right)^{2} \right) \, \mathrm dx = 0. \tag{1}$$
Since $$H_{0}^{(1)}(xe^{i \pi}) = -J_{0}(x)+iY_{0}(x) \, , \quad x >0, $$
we can rewrite $(1)$ as $$2 \int_{0}^{\infty} \left(2J_{0}(2x)^{2} -J_{0}(x)^2-2Y_{0}(2x)^2 + Y_{0}(x)^{2} \right) = 0, $$ and the result follows.