They'll probably have direct connections to each page, maybe even counting the sales live. Or the pages in question will report to ORICON after certain marks have been reached, something like every 100 songs sold.
They might go for the same "weight" system as they do for the physical stores, and only count the largest pages' sales.
I did 1 search on that page, and got this:
http://www.ongen.net/search_detail_a.../at0000000308/
By the way, what sucks about the coming oricon charts is that they will combine cellphone and other digital downloads. I think those two should be split categories, even though both is being paid for.