The Bottom Half has water drain holes in it , and the small air gap where the snorkel fits will also allow water to drain if it ever gets into the system . As the V3 uses the stock OEM route for air it should be as safe as the OEM air box in regards to hydro locking. Even with the addition of the V2 and V3 together the air pathway is the same as stock so if you forge a river, and it floods the engine, it would have done the same if it was OEM stock.
Now to answer the question of the Aux Air intake. Right now I am running the air intake hose above the left front tire. On top the finder liner and just below the the car hood. It is not the best place to get air, but it is easy enough to get to, requires little to no mods and does supply fresh air to the V3. The tip of the hose is above the tire so it would take a lot to have water reach it. If I were to use the punch out in the front bumper like snmjin did then a valve should be used to prevent hydrolock as the punch out is closer to the ground and splashing water can reach it when going through a foot or less of water.
There is nothing better for reliability than stock. Car manufactures go to extremes to make their cars reliable no mater where they are used. The desert or the mountains the car will work great . The after market addresses this by making the car better for your individual needs. What is gained in one place is often at the expense of another area. Examples... the car is made faster, but milage went down. The car handles better, but the ride is stiffer. CAI systems are the exception to the rule, a well designed CAI can increase power and give better milage .. if you can control your lead foot.
I hate this part but.... Now for the small print to save my beans from a litigious society . ...
The V3 is a custom made race item, and is designed for track use only and not for use on the street . The V3 is defiantly not for off road adventures in the dirt, or for crossing rivers or streams. . The user assumes all liability in its use.
The larger hole is the foot and need to be sealed. The small hole in the corner is for water to drain even if it is just condensation. There are 2 or 3 of these small drain holes in the Bottom Half.