The big windows cover several decks, I don't see a problem with them. It doesn't have to be one window-one room. Also, each room would probably have its own gravity generator, hence, you could technically adjust the room so that windows are on top or side! Fans think like Enterprise is on Earth with gravity pulling everyone down at 9.8m/s/s...
As for the saucer deflector, I think that it was a good call. Mr. Probert wanted way too many lounges IMO; he said Ent was supposed to be like an ocean liner.
A Starship like that would have double and triple-redundant systems (as is stated in the manual). It only makes sense that there would be a backup for something like deflector dish. I
In fact, I think it's canon that the navigational deflector is called "Main navigational deflector", indicating other(s).