So I have given some more thought about the very extended time these space ships would have to last. I’m sure they could avoid most impacts. But smaller very dense objects with a combined speed would require too much for protection. So now my current thought is these smaller objects should just slice through the whole ship like butter while causing no other structure damages besides the hole created by its size.
This will still be a major problem, but with this new layout, the ship would survive. Unlike my previous layout that had all the habitable areas bunched up.
Just think of foam or even better the volcanic porous rock that is mostly air. Most if not all the objects would still be stopped by the protection layer of containers. The Ship would be larger but most of the overall size would just be empty space.
No more bunched up habitable containers, rather an endless maze of habitable areas, connecting to each other in many ways. That way if something did slice through, it would be isolated to just those containers or even better just pass right through the empty spaces.
This would also create voids within the ship and outer layers of protection. This would help dissipate the force of the impact and also allow for the retrieval of resources that blew out but was still within the ships whole structure.
In these voids would also be empty containers ready to be moved over any impacts, along with everything needed for quick repairs.
No more single massive gravity tube. Rather each habitable area could have their own. But moving between containers would be gravity-free.
So I first came up with a system similar to my previous design but with 200meter voids but still densely packed. This would give the ship at least a mile wide and many longer. I then gave way to my current design.
This would require 8 sided junction hubs to be built in space than creating a huge web lattice for an even larger ship. But this ship would have randomly placed habitable areas around certain hubs.
These habitable areas would surround a single junction hub. The center area would contain a spinning interior for habitable areas with gravity.
*Update 1/15/2014* New Pictures current design