no beeps
Mine stopped beeping too (a '97GS) but runs fine. A new beeper/buzzer from Seadoo Wharehouse is ONLY $65 or so. Probably can replace it like the previous post said from Radio Shack for less than $10. It's not necessary for it to run fine, only you'll have to keep an eye out for the red warning light if it overheats, you won't hear any warning buzzer which could save your engine from fatal damage if you're not aware of it and keep going 'till it cooks itself to death.
I started to disassemble the plastic housing covering the handlebars to reach it or look for it, and it's a real PIA so I stopped. One of these days I'll probably go after it but for now I just frqeuently gaze down at the warning light.