I think I understand what your asking. But no, it shouldnt be.
Only way there could be water in it is if you killed the motor, then plugged the FAE. In that case the water could only be up the exhaust as far as the boat was under, its about pressures, like how they use a hose with water as a level back in the day. It will prob be moist, but you shouldnt have water pouring out when you disconnect it.
Can i ask why you are bypassing the muffer?