Over the years I've done a lot of body lifts on my own and others trucks and as pointed out they do have good points and bad points.
Expense has always been the most attractive point of a bodylift, but dont skimp when buying a body lift, pay a little more and buy a quality name brand lift.
Before doing a bodylift give thought to how your gonna use the truck (this actually goes for any lift), if the truck is going to be used for hardcore off-road saving and buying a suspension lift might be a better idea due to the gained articulation, if its used for lots of towing no lift at all might be best, if it's light duty wheeling or for looks try to keep the lift (either type) as low as possible so you dont loose the handling. Bigger isnt always better you could end up modifying a truck to the point where it wont do the task's you require most of it.
Bodylifts do need maintenance, even for street driving you should be under the truck at least at every oil change to check the body mount bolts for torque and the body mounts for cracking, this goes for suspension lifts too.
If you regularly haul heavy loads in the bed of your truck remember that a bodylift due to the forces involved just lightened the available payload of the bed.
There are ways around this the best way is to tack weld at scab plates of at least 4"x4" at every body mount for the bed (wouldnt hurt to do the same on the cab and fender mounts either to solve cracking issues).
Either type lift raises the center of gravity for the truck so more cautious driving should be in order after a lift.
Almost every lift affects the towing capacity of the truck, but when relocating bumpers it makes the rear one useless for bumper towing and and the front one will now have a much lower crash rating.
Yes when twisted up in a ditch it will make it easier for the cab and bed to occupy the same space, specifically right below the back window you'll probably get a few dimples.
On some trucks you can leave the front hooks in place, they end up sitting down below the bumper and looking out of place.
You could always relocate them at the top of the frame if their not already there, or make custom spacers to lift them, or my favorite trick is to weld them on the frame a few inches farther down the frame sides so they dont stick out the front and arent as noticeable.
Rear or front reciever hitch's can be custom fabbed to lift them right back below the bumper, if you go this route have a certified welder do the job it needs to be real strong and theres structural changes that need to be though out when doing this.
One of my favorite tricks to do when custom fabbing a reciever hitch is to slide it back along the frame about 3", yea it brings the hitch under the truck a little but it also disburses the trailer weight better and makes for a much better handling trailer.
One of the best materials I've found to cover the gaps with is Pond Liner, you can find it at most Home Depots or Lowes in the darden area. It's not to heavy, doesnt easily tear, and comes in large sheets you can cut out to fit you specific needs.