Well, I'm not much of a jet boat guy, but I have owned a few PWCs in my life and used to work on a couple that we used for near shore chart verification up in Alaska. The work boats with jet drives were great; they had Hamilton Jet Drives that allowed you to run the impeller in reverse to flush out the intake. We used that feature a lot, since poking around rocks in Alaska usually came with a lot of kelp.
I've heard from several guys that you can mimic that in a PWC or small jet boat by putting it in reverse (assuming you have a reverse bucket) and picking up as much sternway as you can, then cutting the engine and raising the reverse bucket to allow water to flow backwards through the jet and out the intake, which will hopefully flush out the weeds. I have never had much issue with weeds where I operate the PWCs though and haven't had occasion to try it out. You'd also need a little bit of maneuvering room to do it.