No real difference in post ride flushing with the supercharger on Yamaha skis. The post ride flush is pretty easy: Get the ski level, hook it up to a hose, start the engine, start the water, let it run for 3-5 minutes, stop the water, then stop the engine.........your done. Once a month or so, I recommend flushing with Salt-Away or similar product, and rinsing the inside of the engine compartment with it. It is also a good idea to spray metal components with an anti-corrosive periodically if you ride in salt water. My favorite products are Fluid Film, Corrosion X, and CRC 656 in that order.
Keep in mind that the supercharger adds moving parts to any ski. For the Yamaha it is gear driven and has a clutch, on Kawasaki skis it is belt driven, and I'm not sure how it works on SeaDoo. So, you have more potential failure points, and more points that will need lubrication, inspection, and periodic replacement. For Yamaha SHO and FZR/FZS models with the supercharger, I have not heard of any major failure problems with the supercharger, but keep in mind this system is relatively new (only out since 2008). There have been problems reported with clutch failures primarily on skis that have been modified for more speed on the Yamaha models.
If speed is not a big issue for you, stay with the non-supercharged models. For Yamaha you only loose about 3 mph. You will save lots of $$$ on fuel, and not have to worry about the supercharger failing.