As far as I know, all bonuses stack additively not multiplicatively. There are also specific caps for how much benefit a bonus can give you. Structure cost bonuses do apply to exploitations and exploitation buildings, including Doomsday weapons. In that case they only seem to lower the Production cost and not Energy/Cosmite costs.
I believe the only bonus that makes a distinction between types of structures is the Civil Engineering Guild, which gives bonus production for City Center buildings only. City Center buildings being anything that is not literally located in an individual sector, including stuff like sector type or exploitation type improvements.
