i dont have SS, but if you are destro player you take the left portal at start to go the ground floor (bottom flag) then you go up the stairs (multiple stairs) to the (middle flag) (the top flag is the button to blow everyone up)
So middle flag room on the floor, is small pie to pick up it takes one second. on the inner circle around the flag is the one spawn point, on the outer circle around the room (still inside the room, just the edge of it) near one of the doorways is the other spawn point...
If you do not see them, either a patch has bugged them or another player as recently picked them up, if you are dominating sc just spawn camp the middle flag area and look for pies in my opinion to get enough to throw at players... after a couple sc you will easily have 100+ pies (10 per a pick up)
I also went and checked for you https://github.com/WarEmu/WarBugs/issues/17101
I got most my pies on the first evening, there's been a few hotfix since... so not sure the current status of pies in SC's