You don't want to build a full enclosure for your engine
for several reasons. The engine
is basically a big air pump which takes in clean air and exhausts air full of pollutants and you don't want to create a closed loop system for this air to travel, it won't run for very long.
If you overcame the intake and exhaust problem, you would be up against the engine overheating
. Engines are designed so that they won't overheat until they operate at extreme temperatures which you would be creating with an enclosed box. At best, this engine might be 25% efficient with the remaining 75% being turned into heat that comes off the block and out the exhaust so you need to dissipate a lot of heat. It will run fine at first since it takes several minutes to get the block up to temp and then it will overheat if you put it in an enclosed space. To get around this, engine manufacturers have used water as a medium to transport heat away from the engine but since this engine is air cooled, that is not an option.
It would be possible to build an enclosed box but you would need to provide lots of airflow to it which takes power and provides a way for the sound to travel.
The ways that engines produce sound are through the exhaust, mechanical noises from the engine itself, and by vibrating its mounts. While hondas are pretty good, start by looking at isolating any vibrations from the engine by seeing how it is mounted. Since most of the noise
comes out the exhaust, that is the next place to look. The noise coming out of the exhaust is very directional so you could consider extending the exhaust to point somewhere away from your vessel (and at the rest of us out sailing). You could also look at a different muffler but this often requires adjustments to the carb. A last option might be to kind of build a sound wall which didn't enclose the engine space but reflected noise away from the cockpit