I can comment on the MEGAN side of things. You’re right that the vdemis_me units are moles/s after that line. The comment before it should be clearer.
The emission rate is instantaneous for the time step. You would either multiply by 3600 to get an estimate of the hourly emissions, or accumulate each time step’s emissions and sum them up every hour for perfect accuracy. I’m not sure how BEIS does it but my hunch is that the estimate will be extremely close to the actual value.
Are you using BDSNP or YL for soil NO?