I think if you can cover sensitive components from road spray, there should not be too much risk from rain. The one thing I worry about is the throttle- Mine is up on the bars, has 3 LED lights (it is an older WE brushed 36V hub with Hall sensor throttle). I carry the controller in the battery bag side-pocket, and have attached an old 5V computer fan that runs off a DC converter to blow air directly onto the heat sink and out the zipper top of he pocket. It keeps the controller cool even in summer weather. I have good fenders that minimize road spray, and the battery bag sits behind my recumbent seat, which means I shield it with my seat as well.
I got caught in a real storm last fall, riding home 20miles with 70+lb of SLA batteries- I had 30 lb on the rear rack (36V), and duct taped 4 more 12 Ah lead batteries which I dumped in an old "holey" pannier, on the right side of the rear rack. It started raining HARD- I was soaked right to the soles of my shoes within minutes, and I figured- oh well this thing is gonna short out and blow up. Just kept riding. I stopped once to switch over from the (drained 36V to the 48V battery . I was surprised to find, that even though everything got wet, the only thing that malfunction was my (wired) cyclecomputer (water got in the wheel sensor), and even that started working again after 5 miles or so. Everything else worked great, I just emptied the bag to dry everything out once I got home. I now have a rain cover for the rear batter bags and carry a sandwich bag with me to wrap over the throttle.
One thing I almost learned the hard way is that overloading the bike and rack can be dangerous at high speeds. My single pannier made the bike heavier on one side, and the 40lb battery was flopping around because I did not bother to secure it inside the pannier. I also carried all the batteries on a crappy little steel rack that came with the hub motor kit (which I hammered and bent to get into the right shape to fit the recumbent), and which flexed like crazy every time I cornered or hit a bump. I started off wet but happy that the bike was running so well- until I headed down a big hill (wide, 4 lanes, nice smooth pavement, lots of cars, coasting about 35-40 mph). Half way down the bike started oscillating wildly from side to side- I thought I was gonna buy it at 35 mph for sure. I did not know what was causing the oscillations and was afraid hitting the brakes would either make it worse, or lock up the wheels and make me go down. I unclipped from the pedals rode the thing down with my cleats dragging until the road leveled out and I was able to slow and stop. This was the scariest moment I have had on a bike. Oddly, I never had stability problems on dry roads, I just loaded the bike up with lead to get the range I wanted.
I think the combination of overloaded weight, poor traction of wet roads and having the batteries acting like a pendulum in the back caused this- I have not experienced it again. Since then I have built a sturdy rack and avoided putting a big unbalanced load on the back. I used to run 2 36V batteries in parallel to minimize voltage sagging, but now I am using 48V system with 4 SLA's mounted in the midline. Getting rid of the lead for lighter batteries would help too.