Only problem I know of with the 06-08 FX HOs is there is a potential for the hose clamps to come loose. Yamaha has not issued a recall, but something they call a "Code 90". If you take it to a dealer they can run the HIN and determine if the ski needs a hose/clamp upgrade. Its free, even if you are not the original owner.
Other than that, the FX HOs are a reliable, fairly easy to maintain ski, and will give you a great ride.
I think the biggest issues are to make sure it has been maintained, number of hours, and amount of salt water use (look for signs of corrosion).
Take if for a test ride, and if it does well in the water, you can be pretty sure you have a good ski. Running it on a hose will not tell you whether the pump system is OK or not.