The Magic is going in drydock, btw, not the Wonder. I don't think they're doing anything out fo the ordinary with the Wonder while the Magic is drydocked; they simply didn't take any bookings for the Magic while she's out of service.
Drydock is a a process where they bring it into dock, and pump out the water. It is a required safety inspection by the maritime organizations. In this case they'll be cleaning the lower hull(the red part), giving it a fresh coat of paint. On the inside, they check all the safety equipment, make any updates as needed. They'll also give the ship a good once over, fixing on any things needed.
They are also taking advantage of this drydock to do some remodeling. The ESPN club moves to Off Beat, with a cheers-type theming, The Teen club moves to the old ESPN club on deck 9, and Common Grounds becomes a Coffee bar.
And yes, they will be repairing the stack properly at this time as well.