In a conventional ship you have an engine -> transmission-> drive shaft -> propellerNot necessarily. I'm not a naval engineer or anything but as far as I understand it, with mechanical transmission you have two sources of noise: the transmission, and the engine, both of which can be isolated from the hull by rafts even if they are connected to each other physically. In IEP, you also have two sources of noise: the electric motor, and the engine, both of which also can be isolated from the hull by rafts. I think which one is quieter in the end is whether the electric motor is quieter or the transmission is quieter rather than the fact that IEP has two separated sources of noise. I would amateur guess that an electric motor would be quieter compared to a mass of gears grinding each other along.
Even if the engine and transmission is placed on rubber dampeners to reduce noise the engine vibrations will still be transmitted to the ship's hull through the drive shaft. There's no way around it.
In an IEP system there is no drive shaft.
(maybe in the shipping world the proper term is propeller shaft not drive shaft but you get the idea)