Can a stopped shell still damage machinery?

Would the impact still damage a ship's internals even if modern armor stopped the shell?

Yes, especially fittings, although modern cushioning and rafted machinery could reduce the transmitted shock.

Stopping penetration would still leave the ship to absorb an impact. Internal fittings could break even if the hull and major components used improved alloys. Modern cushioning and rafted machinery mountings could reduce that damage. Machinery rafting is associated with noise reduction, but the answer also gives it a protective role against shock.