With one you lose a body part when ignited.
The other just puts the igniter out.
A balloon full of Hydrogen is a balloon full of molecules.
A balloon full of helium is a balloon full of atoms.
Are you implying that hydrogen is not an atom ?
Yes atomic hydrogen is very rare on the surface of the Earth. But it does exist.
@corlin
The question posits hydrogen in a balloon, not in some special circumstance.
It is possible to force helium into a molecule at millikelvin temps, but that is a special condition.