Dead sure.
Just an update on this, for anyone who's posted here or is interested; I went back to the same base and docked, and again went into the hanger. This time, I watched my notification panel in the top right, and I saw the "Emergency Oxygen Replenished" message. So the answer is yes, planetary bases DO in fact refill your life support's O2 in the hanger. Seems I ran afoul of what appears to be an isolated glitch. Unfortunately it was a glitch which cost me about 4 mil, but hey, life goes on.
Now here's a question I've been thinking about due to all this; why should you even have to go into the hanger for the O2 to refill?!? If the maintenance crews can repair everything on the ship while you're sitting on the pad, why aren't they hooking up a hose and topping you off? Shouldn't making sure your life support system is perfect (since as the as the name implies it's what keeps you alive in the dead of space) be top priority?
Having to enter an area with an atmosphere to replenish your emergency life support O2 (instead of having it refilled when repairing your ship) strikes me as illogical and a needlessly punishing mechanic for new players not aware of it.
Have you filed a bug report and a customer service ticket for the loss? It might be too late for the loss but it can't hurt to try.