I have seen some vids where an assasin IS flying while cloaked, look here:
-watch this "aerial pvp" vid:
(you can see it 2:33-2:50, and if u look closely at 2:48 u see that he has the wings on, and he is on "stealth mode" or w/e.....)
-OK, u can clearely see here taht YOU CAN go on "stealth mode" while flying
(look from 3:50 +...it is on "stealth mode" for some time, WHILE FLYING)
So I think we can stop questioning this, it can be clearely seen, especially in the 2nd vid, u can be on stealth mode while flying (or w/e)