Well, if you look at the drawings (http://www.airbus.com/product/a380_cabin_layouts.asp
) of the upper deck the outer parts seem to slope quite a bit, but the deck is wide for the number of seats so the window seat will not really have a low ceiling. There might, however, be some space between the seat and the actual fuse (by the floor, that is).
A380 upper deck seating is 2-4-2, with a width of 19'5" or 5,92.
A330/340 seating is also 2-4-2, with a width of 17'4" or 5,28m
Tthat's over two feet more with the same number of seats. So any low ceilinged section at the edges will not be a problem. Just leave the last foot clear.
"There are no stupid questions, but there are a lot of inquisitive idiots." - John Ringo