For some reason, Mathematica can handle the problem when represented as one-dimensional distributions, which is allowed given your covariance matrix is diagonal.
$E[y]$
Assuming[k > 0,
Expectation[
(x1x x2x + x1y x2y)/((x1x^2 + x1y^2) (x2x^2 + x2y^2))^(1/2),
{x1x \[Distributed] NormalDistribution[0, 1],
x1y \[Distributed] NormalDistribution[0, k],
x2x \[Distributed] NormalDistribution[0, 1],
x2y \[Distributed] NormalDistribution[0, k]}]
]
$0$ (as it should, based on symmetry arguments)
$E[y^2]$
Mathematica has difficulty solving for the general case when $k>1$ and $k<1$, but can do each individually (and they give the same answer):
Assuming[k > 1,
Expectation[(x1x x2x + x1y x2y)^2/((x1x^2 + x1y^2) (x2x^2 + x2y^2)),
{x1x \[Distributed] NormalDistribution[0, 1],
x1y \[Distributed] NormalDistribution[0, Sqrt[k]],
x2x \[Distributed] NormalDistribution[0, 1],
x2y \[Distributed] NormalDistribution[0, Sqrt[k]]}]]
$\frac{k+1}{(\sqrt{k}+1)^2}$
and
Assuming[0 < k < 1,
Expectation[(x1x x2x + x1y x2y)^2/((x1x^2 + x1y^2) (x2x^2 + x2y^2)),
{x1x \[Distributed] NormalDistribution[0, 1],
x1y \[Distributed] NormalDistribution[0, Sqrt[k]],
x2x \[Distributed] NormalDistribution[0, 1],
x2y \[Distributed] NormalDistribution[0, Sqrt[k]]}]]
$\frac{k+1}{(\sqrt{k}+1)^2}$.
An explicit check for the case $k=1$:
Expectation[(x1x x2x + x1y x2y)^2/((x1x^2 + x1y^2) (x2x^2 + x2y^2)),
{x1x \[Distributed] NormalDistribution[0, 1],
x1y \[Distributed] NormalDistribution[0, 1],
x2x \[Distributed] NormalDistribution[0, 1],
x2y \[Distributed] NormalDistribution[0, 1]}]
${1 \over 2}$, which agrees with the general case.
Expectation[x1.x2/(Norm[x1] Norm[x2]), {x1, x2} \[Distributed] MultinormalDistribution[{0, 0}, {{1, 0}, {0, k}}]]
and likewise for the $E[y^2]$ case. Unfortunately, Mathematica cannot solve these in this form. $\endgroup$