Sage does not offer a "selection" based on quantity on hand in Inventory Physical Count. 

I have had some success in the past to use the Cycle Count Field for this purpose if you don't already use it for true cycle count processing.  In our case the client did not use Physical Cycle Counts, so instead we set a value of "X" in CI_Item.InventoryCycle for only those items with a quantity on hand and then froze only Cycle Count = X.  This can work if you correct the items by refreshing the cycle count of all items to a "  "  (blank) and then freshly reset to "X" each time you want to freeze your inventory. 

Cycle counts is a great way to control the Physical Count process... but systemically excluding items from consideration comes with the risk of not counting something that you have on hand.