Namor was attacked directly due to his hand in killing Dr Spectrum's Earth.
Atlantis was attacked and demolished for the threat the Squadron Supreme (rightly or wrongly) percieved that nation of posing to the rest of the world.
They make that pretty clear in their diatribe they aim at Namor whilst he fights to save his people.
Atlantis had nothing to do with destroying Dr Spectrum's world but the Atlantean forces that attacked Wakanda alongside their Phoenix Force empowered King, did so of their own free will, thus leaving them open to retaliation.
Why this is hard for some to understand is beyond comprehension.