Having the ship being oriented the way it is, I doubt the lack of an easily distinguishable top or bottom would be terribly disconcerting for the viewer once they understand that. in reality. neither are. Whatever side is 'up' in any particular scene will be 'up' to them.
Odd you mention the windows, I wrote a short post about them, but got distracted and never posted it. I do find them somewhat 'upsetting' for the scale. Perhaps the portholes, combined with visible 'shield doors' to close over the observation windows could help to distinguish them as larger than a standard window.