Lincoln and Hive are shown experiencing zero gravity. There is still a great deal of gravity beyond Earth's atmosphere; astronauts experience zero gravity because their spaceships are in orbit, traveling so fast that they're in a constant state of free fall. In point of fact, the Zephyr would have started falling back into the upper atmosphere the moment the thrusters stopped.
Since a thermonuclear bomb burns at over 180,000,000 degrees Fahrenheit there was really no danger at all of ANYTHING surviving the blast- either in Earth's atmosphere or in space.