We all know that Starfleet designs its starships so that the crew can enjoy the miraculous wonders that empty space has to offer. Take the 1701-D for an example. They position the bridge in vulnerable places, offer a nice observation lounge for senior staff meetings, have Ten Forward for recreation and the occasional great stately dinner, and also have many a crew quarter featuring a scenic view. There are certain drawbacks to that however that have been discussed before.
In times of danger however, such as the power outage in episode TNG 1x05 The Last Outpost would it not be wise to retreat to the inner compartments of the ship? Due to the power loss the ship is reported to cool down but physics tells us that a spherical* spaceship put into the vacuum of space loses heat by radiation only. Obviously the inner parts of the ship could maintain higher temperature levels for a longer time while heat is transmitted to the outer shell by means of heat conduction (and convection if you will). Are there really no shelters burried in deep the belly of the ship?
* I think that we can safely assume the shape of the Enterprise to be spherical.