When Sheppard launches his missiles at the darts prior to boarding the hive, he says "Fox four." This is an obsolete term for firing guns, not missiles. The current code for firing cannon air-to-air is "Guns, guns, guns."
Unless there had been a serious fire, a ship that size, with a complement of 200 people, would have air for weeks, before carbon dioxide levels would become dangerous - or oxygen levels low enough.