The silicone will contain acetic acid (unless you use the very expensive stuff intended for microwave circuits) so i say keep it away from the bearings. As long as you grease the shaft...white lithoum grease...well. & the motor end is above the waterline, then you dont need to seal it as you will get very little water getting thru the shaft tube into the hull.
I have bedded a shaft tube in silicone where it comes up thru the keel into the hull, however i made sure there were no electronics in the hull until the RTV silicone had cured...no servo, no ESC, no lighting switch, NO RECEIVER.
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