I think just dealing with the bivariate case is all that is necessary as you're only interested in covariances. I also think that there is likely no analytic solution when the means of the $X$'s are not zero. Here is an approach using Mathematica:
For the bivariate case $Y_1$ and $Y_2$ both have means that can be calculated by integrating over 0 to $\infty$ using the marginal densities of $X_1$ and $X_2$, respectively.
Find the means of $Y_1$ and $Y_2$:
mean1 = Integrate[y1 PDF[NormalDistribution[0, σ1], y1], {y1, 0, ∞}, Assumptions -> σ1 > 0]
(* σ1/Sqrt[2 π] *)
mean2 = Integrate[y2 PDF[NormalDistribution[0, σ2], y2], {y2, 0, ∞}, Assumptions -> σ2 > 0]
(* σ2/Sqrt[2 π] *)
Now the covariance depending on if $\rho$ is positive or negative:
pdf = PDF[BinormalDistribution[{0, 0}, {σ1, σ2}, ρ], {y1, y2}];
covρPositive = FullSimplify[Integrate[y1 y2 pdf, {y1, 0, ∞}, {y2, 0, ∞},
Assumptions -> {σ1 > 0, σ2 > 0, 0 < ρ < 1}] - mean1 mean2,
Assumptions -> {σ1 > 0, σ2 > 0, 0 < ρ < 1}]
(* (σ1 σ2 (-1 + π ρ + Sqrt[1 - ρ^2] - ρ ArcCos[ρ]))/(2 π) *)
covρNegative = Integrate[y1 y2 pdf, {y1, 0, ∞}, {y2, 0, ∞},
Assumptions -> {σ1 > 0, σ2 > 0, -1 < ρ <= 0}] - mean1 mean2 // FullSimplify
(* (σ1 σ2 (-1 + π ρ + Sqrt[1 - ρ^2] - ρ ArcCos[ρ]))/(2 π) *)
As a check one can set values for $\sigma_1$, $\sigma_2$, and $\rho$ and take random samples:
n = 10000000;
parms = {σ1 -> 1, σ2 -> 7, ρ -> -1/2};
x1x2 = RandomVariate[BinormalDistribution[{0, 0}, {σ1, σ2}, ρ] /. parms, n];
x1x2[[All, 1]] = Max[0, #] & /@ x1x2[[All, 1]];
x1x2[[All, 2]] = Max[0, #] & /@ x1x2[[All, 2]];
(* Sample estimate *)
Covariance[x1x2][[1, 2]]
(* -0.7329134893798569 *)
(* True covariance formula *)
(σ1 σ2 (-1 + π ρ + Sqrt[1 - ρ^2] - ρ ArcCos[ρ]))/(2 π) /. parms // N
(* -0.7325923679884647 *)
The results are consistent for this example.