I seem to remember that the standard secret door system looks up the saving throw to determine the search DC. Other than that I don't think saving throws are used at all. They definitely do not factor in to the default FortitudeSave() command which they will always fail.
EDIT: Actually the on-hit knock property may use the fortitude save against its DC. Strike that on hit: knock checks the Unlock DC. Looked at SoU and HotU. Their secret door scripts use the Reflex Save as the maximum detect range, and Will Save as the search DC. Fortitude save is not used.