An interesting problem :) The answer is indeed $\pi$.
The sum is not absolutely convergent - the order of summation counts, and the value of the sum (the sight) depends on the order of summation.
Using the fact that at any fixed $N$
$$\sum_{j=1}^N\left( \sum_{n=1}^N\frac{1}{n^2}\ln \left( 1+\frac{n^2}{j^2} \right)-\frac{1}{j^2}\ln\left( 1+\frac{j^2}{n^2} \right) \right)=0$$
and that at any fixed $N$ the sums
$$\sum_{j=1}^N \sum_{n=N+1}^\infty\frac{1}{n^2}\ln \left( 1+\frac{n^2}{j^2} \right)\,\,\text{and}\,\,\sum_{j=1}^N\sum_{n=N+1}^\infty\frac{1}{j^2}\ln\left( 1+\frac{j^2}{n^2} \right)$$
converge (please, see the addendum), our sum becomes
$$S=\sum_{j=1}^{\infty }\left( \sum_{n=1}^{\infty }\frac{1}{n^2}\ln \left( 1+\frac{n^2}{j^2} \right)-\frac{1}{j^2}\ln\left( 1+\frac{j^2}{n^2} \right) \right)$$
$$=\lim_{N\to\infty}\sum_{j=N}^{\infty } \left(\sum_{n=N}^{\infty }\frac{1}{n^2}\ln \left( 1+\frac{n^2}{j^2} \right)-\frac{1}{j^2}\ln\left( 1+\frac{j^2}{n^2} \right)\right) $$
$$=\lim_{N\to\infty}\sum_{j=0}^{\infty } \left(\sum_{n=0}^{\infty }\frac{1}{(N+n)^2}\ln \left( 1+\frac{(N+n)^2}{(N+j)^2} \right)-\frac{1}{(N+j)^2}\ln\left( 1+\frac{(N+j)^2}{(N+n)^2} \right)\right) $$
$$=\lim_{N\to\infty}\frac1{N^2}\sum_{j=0}^{\infty } \left(\sum_{n=0}^{\infty }\frac{1}{(1+\frac n N)^2}\ln \left( 1+\frac{(1+\frac nN)^2}{(1+\frac j N)^2} \right)-\frac{1}{(1+\frac j N)^2}\ln\left( 1+\frac{(1+\frac j N)^2}{(1+\frac n N)^2} \right)\right) $$
$$=\int_1^\infty dy\left(\int_1^\infty dx\left(\frac1{x^2}\ln\Big(1+\frac{x^2}{y^2}\Big)-\frac1{y^2}\ln\Big(1+\frac{y^2}{x^2}\Big)\right)\right)$$
where, integrating by parts,
$$\int_1^R dx\left(\frac1{x^2}\ln\Big(1+\frac{x^2}{y^2}\Big)-\frac1{y^2}\ln\Big(1+\frac{y^2}{x^2}\Big)\right)$$
$$=-\frac1x\ln(x^2+y^2)\,\bigg|_{x=1}^{x=R}+2\int_1^R\frac{dx}{x^2+y^2}-2\ln y-\frac x{y^2}\ln(x^2+y^2)\,\bigg|_1^R+\frac2{y^2}\int_1^R\frac{x^2}{x^2+y^2}dx+\frac2{y^2}(x\ln x-x)\,\bigg|_1^R$$
Taking the limit $R\to\infty$
$$\int_1^\infty dx\left(\frac1{x^2}\ln\Big(1+\frac{x^2}{y^2}\Big)-\frac1{y^2}\ln\Big(1+\frac{y^2}{x^2}\Big)\right)=\ln(1+y^2)-2\ln y+\frac{\ln(1+y^2)}{y^2}$$
Integrating with respect to $y$
$$S=\int_1^\infty\left(\ln(1+y^2)-2\ln y+\frac{\ln(1+y^2)}{y^2}\right)dy =\pi$$
$\bf{Addendum}$
In order to skip the pairs $(j,n)$ such that $1<j\leqslant N, \,n>N+1$ and $1<n\leqslant N,\,j>N+1$ it is enough to ensure that both sums $\sum_{j=1}^N \sum_{n=N+1}^\infty\frac{1}{n^2}\ln \left( 1+\frac{n^2}{j^2} \right)\,\,\text{and}\,\,\sum_{j=1}^N\sum_{n=N+1}^\infty\frac{1}{j^2}\ln\left( 1+\frac{j^2}{n^2} \right)$ - converges.
Indeed,
$$\sum_{j=1}^N \sum_{n=N+1}^\infty\frac{1}{n^2}\ln \left( 1+\frac{n^2}{j^2} \right)<N\sum_{n=N+1}^\infty\frac{\ln(1+n^2)}{n^2}=F(N)$$
$$\sum_{j=1}^N\sum_{n=N+1}^\infty\frac{1}{j^2}\ln\left( 1+\frac{j^2}{n^2} \right)<\sum_{j=1}^N\frac{1}{j^2}\int_{n=N}^\infty\ln\Big(1+\frac{j^2}{n^2}\Big)dn$$
$$<\sum_{j=1}^N\frac1{j^2}\left(2N\ln N+N\ln(N^2+j^2)+j\arctan\frac jN\right)=G(N)$$
where both functions $F(N),\,G(N)$ are finit at any fixed $N$.
It follows that we are allowed to change the order of summation $(n,j)$, what provides mutual cancellation of all terms $1<j\leqslant N, \,n>N$ and $1<n\leqslant N,\,j>N$ of the desired sum $S$