Ok i made it to sotha sil clockwork city today, and went up and clicked his body (no inventory either) and his mask is not there. Where could it be?

have you installed a mod that adds his mask to the game? vanilla morrowind doesn't include a sotha sil mask.

sorry, didn't know godly masks was a specific mod

You may have a plugin in your load order that comes after "Godly Masks" that redefines the gods and overrides the change made by "Godly Masks". You could try merging objects or moving "Godly Masks" lower in your load order. Or post your load order and maybe it will be obvious to someone.

Edit: Oh, and looking inside the mod, Sotha Sil's mask is carried by Almalexia.