This thought just came to me and I figured this would be the best place to get an answer. Given the time period, I would assume that most men on board were smokers. Was it allowed? If not, did sailors smoke anyways?
Smoking was allowed but only when the submarine was at the surface never when it was submerged. There is an interesting first person account of submarine life during WWII where a sailor called Derek Traylen in the British royal navy wrote "Of course smoking is not allowed when dived, but we may smoke on the surface except on the bridge as a lighted cigarette could be seen for miles." I'll link the source below but for an interesting fact smoking on modern subs was just banned in the United States of America on December, 31, 2010.
http://www.bbc.co.uk/history/ww2peopleswar/stories/72/a4167272.shtml first person account
http://www.cnn.com/2010/US/04/09/navy.smoking.subs/ modern smoking ban
On a related note, here's what can be used if oxygen levels in a submarine or aircraft drop too low, due to fires or smoke (not smoking cigarettes):