When it comes to staying warm in nasty weather, be it cold or rainy or both, nothing beats an outer layer that has a hood on it. The hood keeps the elements off of your head, but more importantly it blocks the wind and keeps your neck warm which you can't always do with a hat/beanie and scarf/buff combination if it is windy and damp. A hood also helps keep all of the heat inside of your clothing system, just like the drawstring closure at the top of a mummy bag keeps the heat inside from getting out.
Having said that, let's get back to your question. If you plan to use the puffy/insulating layer as an outer layer then I would go with a hood. But most puffy jackets aren't designed for outer wear in terms of durability and water repellency, so they are normally worn under a weatherproof outer layer, which is why they often do not have a hood since they are an inner insulating layer.
My preference and my practice is to use a puffy with a hood if I can, even if it is worn under an outer weatherproof layer. I don't see laying the hood flat under my outer jacket if I don't need it as a problem, but some folks don't like it that way. I will wear the puffy hood and then add the outer layer hood over it. For years in the winter I would wear an old TNF down jacket (that had a hood) under a rain jacket shell as an outer layer. Nice and warm, no wind gets in, and I am a happy camper.
Larry