Today I have a newer Honda Foreman in the shop. It went through the ice and spent a bit of time upside down and submerged in salt water. The driver was cold and wet, but she is ok.
The top of the engine was full of water. I pulled the spark plug and the water ran out of the cylinder. I had to remove the exhaust to get the water out of the lower bends in the pipe and the muffler. The throttle, choke and brake cables were also frozen. The rear drum brake (that never works anyway on these things anyway) was filled up. The gas tank and the carb also needed to be cleaned out. Somehow the oil in the crankcase and the front and rear differentials did not have any water.
For most of the mechanical system being submerged is not a problem. The real problem is the electrical system. The machine was sunk in salt water, which is very corrosive. Once that salt gets into the connectors there is no way to get it out. It does not cause immediate problems, but I am expecting that this machine is going to have a lot of faulty corroded electrical connections in the years to come. The salt can also be a problem in carburetors. The salt deposits block up the jets and small passages and they cannot be dissolved, they must be scrapped or picked out. Sometimes it is impossible to get rid of it all and the jets must be replaced.