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You can use dielectric grease on connections to keep water out, you can also use Silicone II (non reactive to copper) on connections to seal them up completely, controllers should either be weather tight and sealed at the factory or they should be inside the vehicle, but most controllers are weather tight.
Motors should have sealed bearings, if they don't then dust is going to be more of an issue then anything else.
As for water in the motor, most motors are not designed to be run in water for, but it will not hurt them as long as they have a chance to dry out at some point.
Take a look at your car alternator, it's not even close to being sealed up and if you look at it after driving in the rain you will find it soaked, some trolling motors are water cooled and the only thing you have to watch out for with them is not to use them in salt water.
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