do you have a tach or are you just guessing at RPM?
you keep saying speed, so I have no idea if you mean boat speed across the water or RPM.
there is no reason I can think of that a motor would make a loud noise like a muffler fell off when it just lowered RPM.
motors make more noise at higher RPM
I would hook up a timing light to see what the spark timing is doing at low and high speed to see if it is stays in spec
maybe if an intake valve stuck open it would fire back thru the intake making a loud noise.
and make sure all the timing marks still line up on crank and cam