Welcome to the 21ec fraternity. I spent a lot of money and effort to quiet my 21ec down, with modest success. My father worked in the field of occupational health noise reduction, and I absorbed some of his knowledge along the way.
Noise is energy transmitted from a moving object, be it a loudspeaker cone, violin string, or whatever. It can set a receiving object (our ear drums) to vibrating. I have a Volvo engine in my 21ec. I imagine the Yanmar probably makes similar noise. The first step in keeping things quiet is to mount the engine on rubber "feet" that will reduce the amount of vibration transmitted to the hull. The factory did that. We can't improve on it. My Volvo seems to vibrate more than I would hope for. Diesel engines have very high compression, and their power pulses are sharper, more abrupt than gas engines. Sad to say (because I like diesels) gas outboards are much quieter. At certain speeds, the engine vibration sets all sorts of things to shaking and rattling. There's not much that can be done about that. Basically, the whole boat vibrates.
Higher frequency noise can be absorbed by enclosing the engine in a box with sound absorbing lining. The factory lining seems to be just foam rubber with a foil facing. It is almost useless. A company in Salem, Mass sells a sophisticated lining material, with a heavy vinyl layer sandwiched between two foam layers. The idea is that the sound from the engine will try to make the heavy vinyl (they used to use sheet lead!) to vibrating, but it is so heavy that it just absorbs the sound energy and doesn't vibrate much, thereby not transmitting the sound to the outside. It works very well for higher frequency sounds, but can't do much about the low frequency noise from the engine. I spent several hundred dollars on their product, and I would say it helped some, but not whole lot. Company's name is Sound Down.
I have come to just live with the little diesel's noise. There are certain RPM "sweet spots" where I find the vibration reduced and the noise less bothersome. I try to cruise there.
I would suggest and hope, that you can get used to the noise. I think you may be disappointed by putting much time, money or effort into reducing it.
Larry