I seem to have ridden quite often in rain, mostly the light to medium stuff, although around Christmas time I had a 5 mile ride that was very very wet indeed, equivalent to cycling up a river bed with an inch or two of water. My controller sits in a box that is part of the bike frame behind the bottom bracket. Glancing down it was as though a hose was pointed directly at where the wires enter the box with the stream of water coming off the front wheel. I full expected the electrics to pack up, but they kept going.
About 3 weeks after this my controller packed up, although I had completed several rides in between with no noticeable changes other than possible brake switch issues mentioned below. At the time I thought it was due to water ingress and the local bike shop cited this as the likely cause. When I examined the old controller there was no evidence of water ingress at all.
In hindsight, I don't believe water was the problem, as I had experienced what I thought was brake switch problems a few times before the soaking took place. In addition, with the new controller fitted all other associated gremlins have ceased and it's running perfectly. This, to my mind, suggests that the controller had been undergoing a progressive component failure for several weeks and I don't think the soaking really had any relevance to the controller failure.
I've ridden in the wet several times since with no adverse effects. Accordingly, at least on my installation (Freego Eagle Hub Drive 250 watt with battery behind the seatpost), it seems very well protected against moisture ingress and I don't concern myself about it anymore.