Re: 98' SeaDoo Gtx limited with hole in resonator (muffler)
I had a hole in my expansion chamber on my 97 GTX. I used marine JB weld and it worked perfectly

But it wasn't below water level like your problem. I'm thinking the resonator is the part that actually looks like a muffler? And for the size of hole, that's a tougher fix. Mine was the size of a pencil - much easier to patch.
Howerver, if it were mine, I would get an aluminum threaded plug from the hardware store. The kind of plug that would be used in electrical junction boxes or outdoor light fixtures. You might find one that diameter. If you do find one, then make sure the resonator is completely dry and make sure that there is no rust or grime around the hole since you won't be able to get the weld to adhere to that stuff, then thread the plug into the hole, then use marine JB weld all around it and don't be shy to "glob" it on. Place some duct tape completely over the fixed area so that it holds the JB weld in place and from dripping off your new patch. Position the resonator, with the hole on the bottom to dry, and without letting the patch area touch anything. Let it cure for 24 hours. Then give it a water test by plugging one end with your hand and filling it up with water. If it doesn't leak, then it's worth a try on the lake. Good luck!