Since energy suppliers meter their output to apply a price, I'm wondering how hidden costs could exist (unless the software is somehow circumventing or undermining the meters?).
I would think it'd be pretty straight-forward experiment to use software from the late 80s / early 90s for a couple weeks, measure machine energy consumption, then compare with the consumption from a machine running the latest version of everything for two weeks. Next month repeat but also use a processor from the 90s for the first two weeks. Rinse, repeat, extrapolate, apply statistics, &c. Maybe try adjusting for or comparing differences in appliances common then and now.
If software energy costs are somehow hidden, I can only think they're hidden because we're deliberately not choosing to look at them.