Red, thats a great looking boatI feel the guy at performance jet is a complete moron and i would stop all dealings with him. The hole you are talking about is where the water drains out of the header when you turn off the engine.
85 percent of jet boats run these headers the other 13% run log style or other water jacketed headers because they dont want the noise or the headers hanging out. The other 2% run completely dry because they are drag boats.
A dry header tube header is dangerous unless on a drag boat.
A pick of my old jetmate after I installed the headers and it is still running the same headers to this day.
Regarding the drain holes in the primary tubes....I was wondering about those, they just drain down into the bilge? Is there much water coming out, or does the heat dry most of it up quickly?