Hyper Cache Configuration

Hyper Cache plugin works just fine with EDD, even on Multisite, if you add these URIs to the  Hyper Cache Options -> Filters section -> URI to reject:

/downloads
/downloads/
/checkout
/checkout/
/purchase-confirmation
/purchase-confirmation/

Variation: If you change the default pages for options 2, 3, and 4 in Downloads -> Settings -> General, then edit the URIs above to reflect that.