I am a wuss, and don't ride at night or in the rain.
I wouldn't leave the bike in the rain, more for protecting the seat, and preventing rust than anything.
An air-cooled motor spins, throwing water out the same way a lettuce centrifugal dryer does.
Most PWM controllers are epoxy sealed and batteries aren't too picky about rain. Rubber boots over the ends of the battery cables are always a good idea.
Here's my bike from the big energy fair this summer. Notice the ominous clouds in the background?
Ryland (guy with the solar shirt and green CommutaCar) went out for a ride on my cycle at the end of the day and got caught in a huge down-pour for 5 or ten minutes. No ill effects on the cycle, although Ryland seemed to enjoy the ride.