Just a couple of points... There is not enough suction on that hose to suck up anything, especially water. You have to remember, the airbox is still open to the fender well. Unless that is blocked off, air will come in that way even if the pipe is submerged. I don't see that as an issue.
Second, If your filter minder is getting sucked down to 25% with a new filter on a stock truck, it isn't functioning correctly. I've never trusted those, never had one that worked propery in any of the dozens of trucks I have had fitted with them. It is well known that a stock airbox and stock filter can support 500 hp, that is a lot more air moving through than a stock engine. There isn't much of a restriction there at all, the goal of this project is to provide cooler air. Of course cool air is coming through the fenderwell anyway, so I don't really see the point of the modded airbox anyway.