I don't see a problem with a single wheel trailer, people really like
the Bob trailers that have a single wheel, but if you want a larger trailer like
the Bikes At Work trailers and if you want it for hauling stuff then I think that a two wheeled trailer is going to be easier to load stuff on to.
As far as drive wheels, I see a few options, a single wheel drive on a two wheel trailer and design the hitch to be as low as possible so the trailer doesn't knock you over then just live with the effects and handling that it will cause, or you can do a two wheel drive trailer either with a differential from an old ridding lawn mower or go cart, you can buy one new from Northern Tool for $100 and it will weigh around 10-12 pounds, or you can put a free wheel on each drive wheel so the wheel that is going faster freewheels when you go around a corner, this is going to give you some odd handling and is not going to allow regen braking but it would be simple, cheap and light weight.
Another option that might give you the best handling is to mount the electric motor on the bicycle, put the batteries and controller in the trailer with a quick connect plug so you can leave the trailer behind if you want to ride the bike, then you'll be left with only the weight of the motor on the bike.
As for options for your high voltage battery pack, if you don't need a lot of range you could also go with lithium batteries, I have 4 lithium battery packs on my electric bike, they are the 36v (really are 33v) and can be wired up to give you 132v and those 2.6amp hour packs would give you around 10 to 15 miles of range and take up as much space as 4 bricks.