I don't know for a fact, but my theory is;
Before the testastretta engine was released the CPU was mounted underneath the seat unit and in the case of the SPSs were massive units. These needed heat shields on the sides of the CPU and hence would have required some way to get the heat out from under the seat. Hence air vents were designed into the seats.
After the CPU moved to the side of the bike (with the testastreeta engine I think) and was made much smaller, there was no need to have any seat vents, therefore the 998s don't have vents.
So I reckon you can use the 998 seat on your 996 no problem, unless its a SPS, even then you'd probably get away with it anyway.
Tim
