Though the server reboots, anything constructed within the server will remain there indefinitely, so build away!
To obtain more cargo bays, dock at any station, then choose "Enter Station" from the docking menu (F3). Then choose "Shipyard" from the bottom left. Once in the ship customization screen, choose "Frame Config" and you can customize your ship's layout and performance.
When you move up a ship frame, you gain more points to use in the Frame Config area.
Hope that helps!Hail Ghost Fleet!