a hood on outer layer is almost crucial for the wind resistance help but also importantly for the water resistance it adds to the head and neck region.
I agree a hood on the mid or base layer is probably a little over kill. I am happy to pop a beanie on to help those cold mornings or evenings.
But when it starts to rain and even if its mild enough to not warrant rain gear, a beanie isn't stopping water from running off and going straight down the neck and onto the back and chest. A hood prevents this and makes it much easier to go a few minutes to catch some cover or give a few minutes to get into a pack and get out rain gear without getting soaked too badly.