The power behind the Empire was to be big and imposing and strike fear throughout the Galaxy. That's how the Emperor liked to roll. They did learn the lessons from the 1st Death Star. While construction was being completed it was being protected by the force field. I'm sure once it was all done it would've been able to generate its own field. Access to the inners for repairs and stuff meant there had to be big shafts. Otherwise, how are you going to carry out such work? It wasn't meant to be a weakness, they were there for practical purposes.