I know that it is said that since the shuttle bay goes so far down into the ship that it's inconcievable that the Enterprise E could separate. I think that's a little short sighted since by then they relied so heavily on force field technology. I think that since the separation line is still visible on the model in Nemesis, that the shuttle bay could easily be evacuated and opened to the vacuum of space. I also find it likely that retractable bulk heads could be moved into place to protect the shuttles and other valuable equipment from potential harm. Not to mention that, as I stated earlier, there are also several heavy duty force fields that could be activated to protect other areas.
I am still in the camp that the Enterprise E can separate.
I am still in the camp that the Enterprise E can separate.