HOMER gives hydrogen energy storage in the form of mass (kg), what pressure is this at? Can this pressure be manipulated in HOMER? Will I need to use Boyle's law or the ideal gas law in excel with the raw data to change the pressure?
Hydrogen is indeed measured in mass, and the pressure will not affect the usable energy within a given mass of hydrogen. This is because hydrogen fuel cells use a simple fusion reaction, which is independent of pressure.
Basically, if the stored hydrogen is under pressure, it will be released before the hydrogen is utilized for energy production.