Hi, first of all, have you found a solution?
The only thing I could find in the mod files is that, the amount of dark energy depostits is predetermined by the amount of dark matter by the start of the game. At least that's my guess, because I'm not really a programmer. This is the code i found:

acot_d_dark_matter_deposit_3 = {
resources = {
category = orbital_mining_deposits
produces = {
sr_dark_matter = 3
acot_sr_dark_energy = 3

I really don't know if it is possible to add dark energy after the game has already started.

You sir found the missing puzzle piece so I'll share what I have. The console command to add dark energy is: Resource acot_sr_dark_energy then however much you want.

effect add_deposit = acot_d_dark_matter_deposit_3 (3-9) (file acot_orbital_deposits.txt)

write in console:
effect add_deposit = acot_d_dark_matter_deposit_9
can be entered many times