The Crystal Gems may or may not be protected from Shatterbird by the Manton effect. Hard to say for sure.
Maybe, if they’re lucky. Unfortunately for them it’s quite unclear at this point how exactly the Manton effect works, not to mention whether it’s even a thing in the first place. The strongest hypothesis has it depending on the power, which adds another layer of uncertainty as to how the effect works specifically for Shatterbird.
Notably, the Gems are not protected if the Manton effect prevents Shatterbird from controlling silicates in organic beings, but are protected if it operates on the distinction between living vs non-living instead.