there are area's that water and mud can enter the tranny housing. it is not "sealed" to the motor only bolted.
The front bottom half of the tranny has a inspection plate "Dust cover" over it. This cover is also not sealed to the tranny housing only bolted. If you look at the bottom of the inspection plate you will see and opening about a 3/16 inch wid and about 10 inches long at the front bottom of the tranny housing. This is where water/mud/debrie may inter the tranny.
As for "bad" to clutch while in water/mud. yes it is not suggested.
With the water or mud in the tranny....when you clutch (press clutch pedal to the floorboard) the pressure plate releases presure from the clutch disc and the fly wheel.
"opening them up/seperates them"
This can allow water/mud to get inbetween the plate/disc/flywheel.
To sum what will probally happen if you get fluid or mud/debre in there.....you will be replacing them. Fluid on those parts is not good!
hope that helps?