Considering the age your your engine and the fact that you have no records of the supercharger ever being rebuilt, I would not run my engine at all until I had the supercharger rebuilt. The general rule of thumb (if rebuilt with the latest OEM parts) is 2 years or 200 hrs. Since you have a 2005, it is possible you have the older ceramic washers on your supercharger. They are a ticking time bomb. If they let go while the engine is running it will need to be pulled and rebuilt.
My advice is to pull it and have it rebuilt by someone who knows what they are doing and only with the latest Seadoo OEM parts. It is not really that difficult to do from videos I have seen, but it does require some skill and special tools. If done wrong it could destroy your engine. I would not attempt myself, unless I got some first hand experience.
They are not too difficult to take off, only held on by 3 bolts. Being a boat though, they are hard to get to. Search the internet for youtube videos about seadoo superchargers and you will find a wealth of information. Also search this site for "supercharger" and you will find tons of info.
This site offers a mail order rebuild service for a fair price.
http://www.seadooforum.com/showthread.php?70191-Sea-Doo-Supercharger-Rebuild-Service
Seems like you may be new to the world of seadoo, if so welcome. They are good reliable fun boats if maintained properly. There are some issues with some of the older supercharged engines that require specific maintenance protocols or blown engine. Supercharger is one item, and hollow exhaust valves happen to be the other potentially catastrophic issue. Not sure what your level of experience is with engines or wrenching, but do what you can to familiarize yourself with this boat and engine. This site has tons of info, just search the threads. You can also download a copy of the service manual for your boat/engine. Didn't mean to shock you with all of this, just trying to save you from a blown engine.
If you have specific questions, post back and we'll do what we can to help!