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Congratulations, you have just identified problem #1 with MC VaR. Problem #2 is that you want to represent some sort of correlation structure among the assets.
The most straightforward method is to choose some historical data for your n assets, generate the covariance matrix on the excess returns (perhaps by using exponentially decaying weights as you go further back into the past), then use Cholesky decomposition on the resulting matrix. You can then simulate returns by multiplying the decomposed matrix by a random vector of independent standard normals.
This solves problem #1 by assuming that excess asset returns are normal and problem #2 by essentially regressing each asset, in sequence, against the previous ones and then capturing the residual variance in a new factor.
In practice it is common to impose correlation structure via a factor model, where each asset is envisioned as a linear combination of m << n market factors, plus an idiosyncratic risk component. Such an approach may lend some understanding of the interrelation of the assets, but to do it, you need a set of factors; determining these is at least as much art as science. If you're interested in learning about these kinds of approaches, check out the Fama/French factors; French has historical data available on his site.
Have one more question in mind, if we really construct the correlation structure. As far as I understand, to put it simple, it relies on historical data to build some statistics. Then, to put it further simple, the VaR is just a statistical value derived from historical data, is it ?
If so, why don't I use historical simulation to calculate the VaR directly ?
As you know, the drawback of MC is the computational consumption.
For every method, there must be pros & cons. How is the practice in industry ?