Toyota cautions us to keep the area near the hybrid traction battery dry. Yet this morning - upon opening the back hatch for the first time in a week - I found a significant buildup of ice in the roof channel located immediately above where I think this battery is located. (We had an ice storm here earlier in the week) Shades of glacier-ice calving off the roof of Cowboys Stadium? Good thing it wasn't a warm day.
Sounds like the roof channel is doing what it's designed to do: channel water, debris away from the inside of the Prius cargo area. The hybrid traction battery is located under the rear seats, so I doubt that a small amount of moisture inside the cargo area will hurt it. However, the 12v car battery is located in the right side wheel well, so keep that area dry if possible. On a related issue, the filter for the "hybrid traction battery" is located next to the right rear passenger seat on the pillar post. Don't get that area wet, nor blocked.
The hatch seal is -inside- of the water drain channel. There is little chance that water will enter the car. Even if it does, it would have to somehow get through the hatch floor to get at the traction battery. It would pool around the spare tyre first, which is 5-6" below the battery. The 12V battery is not really dangerous if it gets wet (with my previous obsolete vehicles I've always washed the battery when I've washed the car with no ill effects), but again, it's inside the hatch and protected by the hatch seal, as well as being under the hatch floor. I've never found water in quantities large enough to cause problems in either area. Only a few drops have ever gotten in, and when I wash Pearl I'm pretty liberal with the hose, including in the area of the battery vent intake.
It looks to just be an air intake, no filter. Maybe there's a filter downstream? Second Gen's have had dust clogged fans, according to this shop specializing in Prius maintenance: Luscious Garage | Blog | Prius battery cooling fan cleaning, P0A82
As I think about about keeping the hybrid traction battery (HTB) dry, It's possible that two backseat passengers, each with a 32 oz slurpy sitting in the armrest cup holders could spill their drinks onto the back seat; i.e. sudden stop. Since I've never seen the HTB, I don't know how much insulation it has to guard against spillage and/or getting wet. I'm assuming the seat material would absorb most of the liquid. I say this because the owner's manual does say not to get the battery wet. If this is all I have to worry about, I'm thinking life is pretty good for me!