Alas, I think that is how they are intended to work. I never use pyramids anymore, but iirc, the bonus is additive; it only gets multiplied if you add a % buff after applying the Dark Pyramid.

If you have 100 cloak and use a Pyramid, you will have 150 cloak (100 + 50).
If you have 100 cloak, use a Stealth Optimizer, then add a pyramid, you will have 180 cloak ((100 * 1.3) + 50)
But if you have 100 cloak, add a pyramid, and THEN use a Stealth Optimizer, you will have 195 cloak ((100 + 50) * 1.3)

(also, if you have a Pyramid on and then change to Zolazin and/or Spy, you'd likely multiply it, since the 1.4 multiplier buff is added *after* the Pyramid buff. Have never tested it, though)

Tachyon Cylinders and Subspace Seekers work the same way -- they merely add +50 and +175 scan on top of whatever you already have on, but can be multiplied by buffs that are applied later.