Re the benefit of the speed paddlewheel, I wouldn’t want to do without it because of measuring true wind speed.
The masthead wind transducer measures apparent wind speed and direction. Unless the boat is stationary, the only way instruments can give true wind speed and direction is via a calculation that uses speed through the water (not speed over the ground).
So I keep mine clean as others have described. I’ve had both with and without the flap in the past and it’s certainly less dramatic with! Bear in mind that the wheel itself can sometimes be damaged but it’s easy enough to replace with a spare by driving out the securing pin.
I recommend double checking that all is dry a little while after having gone through the whole job. Just in case you got a cross thread or the o-ring got damaged.