Those seats can be used for any additional crewmembers like loadmasters or engineers who might be required at an outstation. Further those seats might be used for deadheading crews or for persons who are needed to be on board e.g. if horeses or any other live stock is transported.
The big number of seats in the upper deck of a converted frighter like the B747-300SF used by KA is only due to the fact that these aircrafts are converted passenger aircraft. The clasic B747F was in general a B747-200 and had only the short upperdeck.
As there is in general no need for a long upperdeck for a pure frighter the B747-400F has only the short upperdeck of the "old" B747-200F.