All wave bonuses are multiplicative. So if you build 2 zenith spacetime manipulators on a plant, you get x4 waves on that planet. Build 3 of them, and you get x8 waves, not x6. Four it's x16, so it adds up fast.
Bottom line is that generally you don't want to use stuff with wave bonuses on planets that might actually see waves incoming. The effects of wave bonuses are always local to the single planet the wave bonus ship is on, so you can safely build as many of those as you want on a planet where there has been effective gate-raiding to all adjacent planets, or to a behind-the-scenes planet.
That's another big advantage of the logistical command stations, is that they give the speed bonus without any wave bonus to the AI (though your economy takes more of a hit with those).