Here we go---
Engine sounds normal------eliminated.
Engine mounts would make a clunk sound when shifting into gear under all conditions----eliminated.
Transmission under the same load in smooth and choppy water-----eliminated.
Transmission mounts would make a clunk when shifting in gear under all conditions----eliminated.
Drive shaft and bearings work the same in smooth and choppy waters-----eliminated.
Some kind of thrust bearing going bad should make noise all under all conditions in forward gear---eliminated.
Might try reverse in choppy water---would unload the thrust bearing.
You say the prop is ok and tight-----eliminated.
I doubt the hull is flexing and causing this noise or you would have noticed it before.
Still there is still one thing that might make a Clatter noise and is connected to the transom.
The
exhaust system might have a loose clamp some where and is banging against something..
-----and the professor was killed in the parlor with the candle stick-----
Please let us know when you find out.