Reporting back:
Testing some cheap aliexpress 3mm red or yellow through-hole LED's, I found they required around 10ua to have decent visibility. Other LEDs that I got from amazon required several hundred microamps to be equally visible. However, running this 25 cent CREE green LED at 1ua at around 2.5v was sufficient to be dimly visible: https://www.mouser.com/ProductDetail/941-C503BGASCB0F0792
Even 500na was enough, though at less than that it becomes dodgy. Part of the credit goes to narrowly focused optics.
Also, 10ms was enough. So, 1ua at 1Hz with a 1% duty cycle means just 10na on average. Not bad! The pulsing actually makes it easier to see than it just being constantly turned on, I presume because of better contrast.
I haven't yet tried it at night, but so far this is already better than what I was expecting a priori. Putting it at the bottom of a black tube might also be interesting to try: you'd get improved contrast, and with the narrow optics maybe little light would be sacrificed to the blackness of the tube
Anyone here found an LED that's more efficient than this one? Or is this already about as good as it's likely to get?