Will open doors, holes in the hull, and hull damage affect flight with the new model?

Not really, but there is a caveat to that, right? For a start, in the interest of this game actually functioning and having a reasonable frame rate, we don't actually simulate all the intricate details of the aerodynamical shape. So when you're in atmosphere and you make a hole in the ship, it's not really going to change much, simply because we just don't simulate to that degree. It's just mostly not necessary. However, if you lose chunks of your ship and the mass changes, that will affect the handling. So shoot it more.