I see what you are asking. I remember reading that much of the commercial hydrogen is derived from methane/natural gas. This does not seem to be different then any other hydro-carbon so when used in a fuel cell it still combines with oxygen producing water. Oxygen is pulled from the air just like an ICE would burn hydrogen so the equation is the same as petrol but cleaner.
I doesn't seem like too big of a concern though. It seems nature has built in
negative feedback loops like if CO2 or water vapor levels get too high then plant life will flourish to take more of it out of the air.