>1. Generally, is this a good/bad idea? Most people use deep boxes for brood. Why?
Because it's what the books recommend and it's what comes in the beginner's kits. Remember, when they were "invented" feed came in 100 pound sacks and 35 gallon barrels were unheard of because everything came in 50 gallon barrels. A full deep weighs 90 pounds. A full medium weighs 60 pounds. A full eight frame medium weighs 48 pounds. Mine are all eight frame mediums.
Standardization is wonderful:http://www.bushfarms.com/beeslazy.htm#uniformframesize
Ligher boxes are wonderful:http://www.bushfarms.com/beeslazy.htm#lighterboxeshttp://www.bushfarms.com/beeseightframemedium.htm
>2. How many medium supers would I need to first start the hive and how many would constitute the brood nest of an established hive?
3 mediums = 2 deeps. 4-8frame mediums = 2 deeps. Here a brood nest for a hive would be 2 deeps or 3 mediums or 4-8 frame mediums.
I would make sure you always have a couple of empty boxes with frames. You might need to super more and you might need to catch a swarm. When you use those, buy some more. No one can predict how many boxes you might need, but you'll most likely need at LEAST five for each hive total.
>3. How many of these boxes would generally be stacked on each other during the honey flow period on an established hive?
How ever many you need. Sometimes you have to harvest early because you can't reach the top box anymore. Sometimes you don't get past four or five.
>4. How many would I want to reduce down to for winter? Or do the bees determine that for me?
I go with the bees. Some of mine are five 8-frame mediums. Some are four, some are three and some are two.
>5. Does this system make it more difficult to rearrange hive bodies to address swarming?
No. It makes it MUCH easier.
> As I understand it, you do not want to rearrange the hive bodies in a way that splits the brood nest area.
I agree, but actually MOST people PURPOSELY split the brood area to prevent swarming. Also called swapping brood boxes.http://www.bushfarms.com/beeslazy.htm#stopswitching
> It seems that having smaller boxes increases the chances that the brood nest is in two or more boxes?
Actually it's LESS likely because you have more choices where to split anything with smaller boxes. With deeps you have less choices where top split anything.
>6. On average do hives with deep boxes for brood nests make more honey or does it affect honey production much?
>7. If I want to start out with nucs, will I be able to find any that fit in a medium super?
Maybe. Maybe not.
> If not, will I need to by package bees with a queen or catch a swarm?
Or put a deep on the bottom or even put a deep nuc on top of a medium box with a board on the side to cover the gap and let them move down into the medium. You can always do a cutout to get from one size to another but I'd just buy the package.