For a Letter of Credit to be honored, the shipment must precisely meet everything specified on the L/C.
Assuming you are confident that the quality will be approved by SGS, I see no reason why you would not comply with the request. If the L/C specifies checking after loading, you will have no option but to do as specified.
L/Cs most commonly require a "clean Bill of Lading", and such a clean Bill would state the actual quantity loaded. In the case of bulk commodities it is not always possible to load a precise weight or volume, and therefore provision may be made for a + or - quantity.
If for some reason SGS are not willing to certify quality, you have a big problem on your hands. For this reason I suggest that it is probably worth your while paying SGS to examine the ore before it is transported to the ship, and then pay again for examination once on board, this time with a certificate issued.