Why would this be so? All of your controls are going to be electronic, your power plant is going to be isolated from the interior ship environment, and most of your jump drive space is going to be occupied by capacitors. Your engine room sounds like a compartment filled with Diesel Engines, not a fusion-powered star ship.
Controls are the least of it. You still need a plethora of systems on a ship in
Traveller. For instance, I did these of an Empress Marava class far trader:
http://www.travellerrpg.com/CotI/Gallery/index.php?n=1285
http://www.travellerrpg.com/CotI/Gallery/index.php?n=1284
http://www.travellerrpg.com/CotI/Gallery/index.php?n=1283
That's just three systems on a small ship. Electrical generators, pumps, motors, compressors, and a whole range of other systems all generate noise and heat in operation. You have a jump capacitor system that stores and discharges megawatts or more of power. That generates heat making all that energy.
The
Star Trek version you imply is nonsense. You still have to have a sanitary waste system. You need a way to treat, heat and distribute potable water all over the ship. You have to generate electricity. You need to lubricate moving / rotating parts with something. Fusion or not, all these secondary systems still have to exist and take up most of the space in your "engine" rooms which are really "engineering" spaces.
A onboard refueling system requires large compressors to turn gaseous hydrogen into liquid. You might need nitrogen to pressurize tanks and oxygen for breathing. Compressors are horribly noisy and hot.
All that stuff needs heat exchangers. Large generators emit a hum at whatever frequency they run at. Ever sit and listen to a 400 Hz one hunt by + / - 5 hertz for hours...? I have. It's annoying like a dental drill.
So, while the rest of the ship might be nice and quiet, the engineering spaces aren't. They also won't have much space to move around in. Open space will be dictated by access to equipment for maintenance and repair. There won't be large open areas as these amount to waste volume that could be spent in a better manner.
Basically similar to the control room on a submarine. Have you ever been onboard of a submarine and seen the control room? Your comments might have had some relevance on the early WW1 boats, but not for the current nuclear boats.
Yes. I'm a Navy nuclear power field Chief (retired). I can still draw an S5G, S5W, or A1W plant mostly from memory. Sub plants are quiet by design, but that comes at a cost. A merchant ship isn't going to pay that cost. A pair of foamy ear plugs are cheaper than noise reducing all the machinery.