you don't want the pod getting wet as it will fall apart! unless of course it is a good K&N or something that are designed to be washed, but all the same you still don't want it soaking. I have seen the pod being installed inside the LHS fender where the original pipe work went. This will prop give you better protection for the pod and colder air.
The hole in the bonnet will tend to suck hot air out as air goes over it. Unless it is more of a scoop, then it will push cold air in. Either way it is OK.