There are two observation decks. One about 1/2 of the way up the tower, the other about halfway between deck 1 and the very top. The stairs of which you speak only go up to the first deck, and it doesn't affect the cost of going up there (about 800 yen last I checked; an additional 600 yen for going to the second deck).
If the weather is bad, the stairs are closed, and it goes without saying that the view won't be very good.