shortage of hydrogen fuels...?

No. hydrogen is quite reactive, so most hydrogen on earth is in the form of compounds. Only in the uppermost atmosphere, on the verge of space, do we find any free hydrogen. And that is at such a low density that it is not a practical source.

Now, there is a chemist who believes there are vast amounts of methane (natural gas) in the earth's crust, and that existing natural gas is not fossil fuel but left over from Earth's creation. Efforts to find such primal methane have not been too successful so far.

There is about one half part per million free hydrogen in the air. It is reactive, but not quite as reactive as one might believe.

If you have done the old lab demonstration where you electrolyze water and catch both gases in a bottle, you will see that the reaction to form water again is neither immediate nor spontaneous under those conditions. (A spark or flame is a good initiator, however.)

Ive never analyzed the reaction byproducts afterwards to see how much hydrogen and oxygen are left, but imagine someone has, and I would expect it to be higher than 0.5 ppm hydrogen. Reactions seldom go quickly to completion.

The inorganic theory of petroleum has been around since Genesis, I guess. I have read it, but am not a believer in it as a serious source of the earth's hydrocarbons.

There is a fair abundance of methane, both bound as hydrates and free in oil production operations. It is made fairly easily by microbes from some carbonaceous sources. Crystalline clathrates are all too abundant in some subsea areas, but mining them for the hydrocarbons is a touchy procedure. Sudden decomposition of methane hydrate can lead to disaster.

If you had a magic filter that could separate the atmospheric hydrogen from the other components with minimal energy, then cheap energy could be a reality. If you could separate gold from seawater in the same way, jewelry and dental work might be a lot cheaper.

There is just no free lunch, is there, Don?

No. Natural conditions cannot be duplicated.

The reactions are certainly not immediate. Still, given billions of years the reactions take place, and hence there is very little primordial hydrogen left. What is in the air and upper atmosphere is continually replentished by the solar wind. But that is still a very low concentration.