The only problem with under the hood is that the heat can sometimes kill the electronics. I had a MSD 6AL mounted under the hood and it didn't last a year. I've had the crane box mounted inside the car for 4 years now and not one problem. I just extended the wires. It keeps it away from the heat and any weather water/snow and all that good stuff.
Put it under the drivers seat, that would be nice and clean....just don't be hoping in with really wet shoes or leave the window rolled down during some rain or something....