If I upgrade a squadmate's ammo power and choose the "squadmate ammo" bonus in level 4, will I and the third squadmate get the ammo at 50% effectiveness? If so, and more importantly, can ammo bonuses be stacked if both squadmates and I have different ammo bonuses with the squadmate ammo upgrade?
No, the squadmate ammo bonuses are not stackable. The ammo power which was utilized the latest will override the effects of any previous one - regardless of whether the powers were the same or not. So in your case, I believe that you'll be able to apply that +50% boost to ammo power to all three of your squadmates. Only once though.