Is a cubic foot of air the same as a cubic foot of hydrogen? It depends on what you mean by “the same.” Naturally, the hydrogen ft[sup]3[/sup] will certainly have less mass than the equivalent amount of air.
Dry gas meters aren’t terribly accurate as flow meters go, but they’re good enough for quasi-governmental (utility) work. The accuracy you can expect depends on where you are in the meter’s rated flow range (the middle is good, and the very bottom end isn’t). Their accuracy curve is generally linear for steady-state flows.
I used to work for a company that makes flow meters. We did thermal, laminar and Coriolis meters; I designed the Coriolis meters. Thermal and laminar flow meters are both really sensitive to different gasses, moreso than diaphragm meters. Coriolis meters, the most accurate type of flow meter, really do count molecules. That is, they’re true mass flow meters.
Thermal meters rely on knowing a gas’ heat capacity, among other things. Laminar meters depend upon a particular gas’ dynamic viscosity, kinematic viscosity and mass. Diaphragm meters don’t care as much what’s flowing through them.
The thing about hydrogen is that it loves to leak out, and that could affect your meter’s accuracy. Hydrogen will tend to diffuse through the diaphragms themselves, making your meter read low. It even diffuses through metal pressure vessels, embrittling them in the process. A balloon inflated with hydrogen will leak down faster than one filled with helium.
Where did you get your meter? Many diaphragm meters are only required to be within +/- 5% or 10% (depending on application), so keep that in mind. Also, hydrogen is a whole lot less viscous than air, so it will flow through your meter more easily (creating less pressure drop) and therefore reading a bit high. But diaphragm meters don’t have a ton of pressure drop to begin with, so it shouldn’t matter much.
The last big caveat is that diaphragm meters are really only accurate for steady-state flows. They don’t do well with flows that vary a lot in a relatively short period of time.
Why are you trying to measure hydrogen flow? If you’re doing chemistry, you probably want to drop $7,000+ on a Coriolis meter. But if you’re just trying to bill your neighbor who’s borrowing a cup of hydrogen for her fuel cell-powered car, the reading from your diaphragm meter is probably pretty close, even without a correction.