Not sure exactly what you're asking. Frankly, I doubt that storage in the voids would be significant in comparison to the overall pond storage, and any flow through the voids would be minor in comparison to the flow over the weir. If the flow is significant, you could use a special outlet device to specify flow vs depth.
I was asking if there was a way to model the flow through the stone before it hits the crest of the weir. But you are correct, this will be relatively minor. This was more a curiosity question.