The 4tec engines are very reliable if taken care of. Seadoo did have a few issues with some engine parts, especially the supercharged versions.
Seems like you understand the supercharger issues. They simply need to be maintained on a regular basis to avoid problems.
Seadoo did have some problems with hollow sodium filled exhaust valves before 2008 (not exactly sure about the date, so don't take my word for it). There were issues with either the metal used or how they were welded together. Either way, on supercharged engines the valve heads have a tendency to break off while the engine is running. It is a bigger problem with boats used in salt water, probably due to accelerated corrosion. It is recommended to have the valves replaced before they destroy your engine.
Seadoo also had some problems with timing chains as well. Not sure what years were affected, but I recall some of the later models 2010-ish. You'll have to dig a little deeper for more information about that.
Any idea how many hours on the engines?
Other than those few things, if the boat was well maintained and it does well on a sea trial you should have a good boat. Be sure to take a good look at the jet pumps and make sure there are no cavitation issues. If you have any other specific questions about these 4tec's post back and we'll do what we can to help.