Other points, since it seemed to hydrolock once....
Was the rear of the boat loaded more heavily than normal?
Were you anchored with wakes or current pushing against the stern?
Most people don't know what the static water line of their boat is, that is how high up would the water come inside the Y pipe when the boat is in the water. Merc has a procedure for how to measure this, and it's worth knowing if your elbows are high enough or not. If not you can add spacers/risers between the manifold and elbow. They have a spec for how high the top of the elbows should be above the actual static water line.
If you find it was from the exhaust, when you take it apart, you have to really make sure that the sealing surfaces are as flat and level as possible. I used a straight edge and feeler gauges to measure the Barr manifolds and elbows that I installed back in 2017. What I installed was a replacement of the OMC one piece batwings, I had to make up my own kit with Barr exhaust parts and V/P downpipes and hoses. It all fit perfect and no leaks inside or out. The manifold and elbow mating surfaces should be flat and level to less than .003" variation. If yours aren't you can take them to a machine shop like SK in Lindenhurst and have them trued up on a belt sander.
I found a way to look inside the elbows with an endoscope camera, by removing a plug in the top of the elbow that VP used for an exhaust temp warning system but any removable plug in the elbow could work. This way after running it, no guesswork, you know if it leaks inside or not. Being that you have a Merc, you could eventually switch to the dry joint system if you wanted too, it's just expensive and you just bought the ones that are on there.
Forgot to mention, you have a 2001, that's a Vortec engine, there were some problems with the intake gaskets, if the gasket by the water ports for the 'stat housing leaks, it will put water right in the oil.
I'd go through the exhaust first, make sure that's not a cause, then re-test. And see if you can figure out a way to measure your static water line. Some people had problems with water up the exhaust after adding heavy items to the stern like an extended swim platform.
Here's a pic of inside the exhaust elbow, after about 4 seasons in salt water....