The exhaust system in the 4-Tecs have an open loop cooling system in them, meaning it draws water in from wherever you are riding to cool them. The engine is a closed loop system, which is cooled on its own system separate from the exhaust (with antifreeze).
Not all 4-Tecs have the intercooler, but if your's does, water is pulled in from the lake, ocean, river, hot tub (yes...a hot tub, watch some youtube) and sent to the intercooler. It then goes in to the exhaust manifold before being expelled out of the ski.
Even 4-tecs without the intercooler still draw water in to cool the exhaust. Even in fresh water, there may be minerals in the water which will adhere themselves to the metal and block the water passages, making your cooling less effective. It is for this reason you still have to flush your wave runner, even if you just ride in fresh water.
The following images are from the 2006 4-tecs and display the water flow of the exhaust system:
With an intercooler, the water first travels to the front (bow) of the engine to the intercooler, then from the intercooler to the exhaust manifold
This engine does not have the intercooler. The water goes directly to the exhaust manifold.
So, if you only ride in fresh water and your wave runner is going to sit for a few days, you are recommended to flush the exhaust system. You always flush the system when you are done riding in salt water.
And when winterizing, you add undiluted (100%) antifreeze into the system to mix with whatever water remains so that it does not freeze, expand, and crack the manifold/intercooler.